species	cell_type	gene_symbol	cell_subtype	sample_type	tissue_type	pubmed_id	journal	title	geo_id
Mouse	Brown adipocytes	"CD31, Vecad, Ucp1, Pparg, Pgc1alpha"	Brown adipocytes	Tissue	Adipose	31087498	Aging Cell	Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging	NA
Mouse	Preadipocytes	"Icam1, Dlk1, Pparg, Fabp4, Cd36"	Committed preadipocytes	Tissue	Adipose	31023895	Science	Identification of a mesenchymal progenitor cell hierarchy in adipose tissue	GSE128889
Mouse	Dio	"Inhba, Tnnt1, Col4a4, Tcf21, Pdgfra, Wnt6"	Dio	Tissue	Adipose	33054397	Arterioscler Thromb Vasc Biol	KLF4 (Kruppel-Like Factor 4)-Dependent Perivascular Plasticity Contributes to Adipose Tissue inflammation	NA
Mouse	Stem cells	"Sca1, CD90, CD146, CD29"	Mesenchymal stem cells	Tissue	Adipose	31087498	Aging Cell	Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging	NA
Mouse	Stem cells	"CD29, Sca1, CD34"	Mesenchymal stem cells	Tissue	Adipose	31340667	Arterioscler Thromb Vasc Biol	Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling	NA
Mouse	Mesothelial cells	"Msln, Upk3b, Krt8, Krt14, Pparg, Cebpa, Plin1, Fabp5, Car3, Cd36, Adipoq, Retn, Adrb3"	Committed preadipocytes	Tissue	Adipose	30265241	eLife	Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult Mouse.	GSE111588
Mouse	Natural killer T cells	Klrg1	NKT1-A	Tissue	Adipose	32516575	Cell Metab	Distinct iNKT Cell Populations Use IFNgamma or ER Stress-Induced IL-10 to Control Adipose Tissue Homeostasis	GSE142845
Mouse	Natural killer T cells	Klrb1c	NKT1-B	Tissue	Adipose	32516575	Cell Metab	Distinct iNKT Cell Populations Use IFNgamma or ER Stress-Induced IL-10 to Control Adipose Tissue Homeostasis	GSE142845
Mouse	Stem cells	"Syto16, CD29, Sca1"	Perivascular adipose tissue-derived mesenchymal stem cells	Tissue	Adipose	31340667	Arterioscler Thromb Vasc Biol	Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling	NA
Mouse	Proliferating cells	"Mki67, Pcna, Top2a"	Proliferating cells	Cell line	Adipose	32294409	Immunity	Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants	GSE102665
Mouse	Proliferating cells	Mki67	Proliferating cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151714
Mouse	Progenitor cells	"Cd34, Pdgfra, Ly6a, Thy1"	Canonical mesenchymal progenitors	Tissue	Adipose	31023895	Science	Identification of a mesenchymal progenitor cell hierarchy in adipose tissue	GSE128889
Mouse	Adipocytes	"Pparg, Fabp4, Hsd11b1, Lpl, Pparg, Cebpa, Plin1, Fabp5, Car3, Cd36, Adipoq, Retn, Adrb3"	Committed preadipocytes	Tissue	Adipose	30265241	eLife	Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult Mouse.	GSE111588
Mouse	Progenitor cells	"Col6a2, Col5a3, Col15a1, Col4a1"	Collagen-rich progenitors	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154048
Mouse	Lymphocyte cells	"Cd3e, Nrc1"	Lymphocytes	Tissue	Adipose	30343900	Cell	High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy	GSE119352
Mouse	Endothelial cells	"CD34, Sca1"	Endothelial progenitors	Tissue	Adipose	31087498	Aging Cell	Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging	NA
Mouse	Adipocytes	"dipoq, Plin1, Car3"	Adipocytes	Tissue	Adipose	31023895	Science	Identification of a mesenchymal progenitor cell hierarchy in adipose tissue	GSE128889
Mouse	Progenitor cells	"Fn1, Loxl2, Tgfb2, Ccl2, Pparg, Cebpa, Plin1, Fabp5, Car3, Cd36, Adipoq, Retn, Adrb3"	Committed Preadipocytes	Tissue	Adipose	30265241	eLife	Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult Mouse.	GSE111588
Mouse	Adipocytes	"Plin, GAD1, GAD2, PVALB, SST, VIP, SV2C"	Adipocytes	Tissue	Adipose	31087498	Aging Cell	Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging	NA
Mouse	Endothelial cells	CD31	Endothelial cells	Tissue	Adipose	31087498	Aging Cell	Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging	NA
Mouse	Muscle cells	"Cnn1, Tagln, Acta2, Myh11"	Smooth muscle cells	Tissue	Adipose	31340667	Arterioscler Thromb Vasc Biol	Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling	NA
Mouse	Progenitor cells	"Dpp4, Wnt2, Bmp7, Pi16"	Interstitial progenitors	Tissue	Adipose	31023895	Science	Identification of a mesenchymal progenitor cell hierarchy in adipose tissue	GSE128889
Mouse	Monocytes	"Hp, Ly6c2"	Monocytes	Tissue	Adipose	31428465	Immunometabolism	Netrin-1 Alters Adipose Tissue Macrophage Fate and Function in Obesity	NA
Mouse	Macrophages	"Folr2, Fcna, Pld3, Lipa, Lcn8, Gpx5, Fcrls, Retnla, Cd209a, Cd81"	Macrophages	Tissue	Adipose	31428465	Immunometabolism	Netrin-1 Alters Adipose Tissue Macrophage Fate and Function in Obesity	NA
Mouse	Macrophages	"Cd14, Adgre1"	Macrophages	Tissue	Adipose	32516575	Cell Metab	Distinct iNKT Cell Populations Use IFNgamma or ER Stress-Induced IL-10 to Control Adipose Tissue Homeostasis	GSE142845
Mouse	Macrophages	"Fcer1g, Ccl6, Mxd1, Tyrobp"	Macrophages	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154050
Mouse	Macrophages	CX3CR1	Macrophages	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151715
Mouse	Macrophages	"CD45, CD11b, F4, F80"	Macrophages	Tissue	Adipose	33054397	Arterioscler Thromb Vasc Biol	KLF4 (Kruppel-Like Factor 4)-Dependent Perivascular Plasticity Contributes to Adipose Tissue inflammation	NA
Mouse	Neutrophils	S100a8	Neutrophils	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151713
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	Cell line	Adipose	32294409	Immunity	Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants	GSE102665
Mouse	Immune cells	Ptprc	Immune cells	Cell line	Adipose	32294409	Immunity	Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants	GSE102665
Mouse	Progenitor cells	"Dpp4, Anxa3, Smpd3, Sema3c"	Pi16 progenitors	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154049
Mouse	T cells	"FoxP3, CD4"	Regulatory T cells (Treg)	Tissue	Adipose	30343900	Cell	High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy	GSE119352
Mouse	B cells	"Ms4a1, Fcer2a, Bank1, Ighd"	B cells	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154051
Mouse	Endothelial cells	"Mmrn1, Egfl7, Cldn5, Kdr"	Endothelial cells	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154053
Mouse	Muscle cells	"Myh11, Lmod1, Notch3, Myl9"	Smooth muscle cells	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154054
Mouse	B cells	Cd79a	B cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151712
Mouse	Dendritic cells	"Flt3, Ccr7"	DC2-like cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151716
Mouse	Dendritic cells	Xcr1	DC1-like cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151717
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151711
Mouse	Schwann cells	"Ncmap, Drp2, Plp1, Stmn1"	Schwann cells	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154052
Mouse	Endothelial cells	Cdh5	Endothelial cells	Tissue	Adipose	33054397	Arterioscler Thromb Vasc Biol	KLF4 (Kruppel-Like Factor 4)-Dependent Perivascular Plasticity Contributes to Adipose Tissue inflammation	NA
Mouse	Muscle cells	ACTA2	Smooth muscle cells	Tissue	Adipose	33054397	Arterioscler Thromb Vasc Biol	KLF4 (Kruppel-Like Factor 4)-Dependent Perivascular Plasticity Contributes to Adipose Tissue inflammation	NA
Mouse	Stem cells	"Klf45, Oct4"	Stem cells	Tissue	Adipose	33054397	Arterioscler Thromb Vasc Biol	KLF4 (Kruppel-Like Factor 4)-Dependent Perivascular Plasticity Contributes to Adipose Tissue inflammation	NA
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Pde3a"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Cish"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Atp5e"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Cyp2e1"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Kng2"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Ryr1"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Atp5e"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Plcb1"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	Adipocytes	"Ucp1, Ppargc1a, Adipoq, Pparg, Dcn"	Adipocytes	Tissue	Adipose	33116305	Nature	snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.	E-MTAB-8562
Mouse	T cells	"Ms4a4b, Trbc2, IL7r, Nkg7"	T cells	Cell line	Adipose	32755590	Cell Rep	Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis	GSE154047
Mouse	T cells	"Cd3d, Cd4, Cd8b1"	T cells	Tissue	Adipose	32783918	CELL	TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy	GSE151710
Mouse	Intestinal stem cells	Clu	Intestinal stem cells	Tissue	Biliary	31080135	Cell Stem Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Stem cells	Tspan8	Mammary stem cells	Tissue	Biliary	31080135	Cell Stem Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Tumor cells	"Spp1, Epcam, Krt19, Cldn3"	Tumor cells	Tissue	Biliary	31080135	Cell Stem Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Epithelial cells	"Cd24a, Cd44, Prom1, St14"	Immature biliary epithelial cells	Tissue	Biliary	31080135	Cell Stem Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Epithelial cells	"Cftr, Slc10a2, Slc4a2"	Mature biliary epithelial cells	Tissue	Biliary	31080135	Cell Stem Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Endothelial cells	"Pecam1, Upk3a, Upk1b, Grhl3"	Umbrella cell	Tissue	Bladder	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Pecam1, Krt5, Krt14"	Basal cell	Tissue	Bladder	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Immune cells	Cd14	Immune cells	Tissue	Bladder	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Mesenchymal cells	"Dcn, Car3, Scara5"	Mesenchymal cells	Tissue	Bladder	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	"Cd68, Cd14, Cd86, Cd163, Csf1r, Lyz1, Lyz2, Fcgr3a, Ms4a7, Fcgr4"	Macrophages	PDX	Bladder	32460812	Genome Med	Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	NA
Mouse	B cells	"Cd19, Cd79a, Cd79b, Blnk"	B cells	PDX	Bladder	32460812	Genome Med	Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	NA
Mouse	Epithelial cells	"Epcam, Krt19, Cdh1, Krt8"	Epithelial cells	PDX	Bladder	32460812	Genome Med	Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	NA
Mouse	Natural killer (NK) cells	"Xcl1, Ncr1"	Natural killer (NK) cells	PDX	Bladder	32460812	Genome Med	Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	NA
Mouse	T cells	"Cd3d, Cd3e, Cd3g, Cd2"	T cells	PDX	Bladder	32460812	Genome Med	Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	NA
Mouse	Primary decidua zone	Ptgs2	Primary decidua zone	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Secondary decidua zone	Ki67	Secondary decidua zone	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Endoderm cells	"Nnat, Apela, Cer1"	Definitive endoderm	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Ectoderm cells	Gata2	Mural trophectoderm	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Ectoderm cells	"Cdx2, Essrb, Eomes, Utf1, Ddah1, Pou3f1, Cpne3"	Polar trophectoderm	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Endoderm cells	"PDGFRa, Sox17, Gata6, Gata4, Foxa2, Sox7, Rhox5"	Primitive endoderm cells	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Ectoderm cells	Krt8	Trophectoderm	Cell line	Blastoid	31846649	Dev Cell	Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid	"GSE134240, GSE123046"
Mouse	Bone marrow perivascular niche	"Vegf-C, Flt4, Kdr"	ECs	Cell line	Blood	32842144	Blood	VEGF-C protects the integrity of the bone marrow perivascular niche in Mouse	"GSE128464, GSE144420, GSE153339"
Mouse	Cfu-e	"Lin-c-kit, CD105"	Cfu-e	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Cluster of differentiation	"Cd107a, Cd107b, Cd200, Cd317, Cd63, Cd47"	Cluster of differentiation	Tissue	Blood	31149730	Eur J Immunol	Single-cell transcriptomes of murine bone marrow stromal cells reveal niche-associated heterogeneity	GSE131365
Mouse	Col2.3	Col1a1	Col2.3	Cell line	Blood	30971824	Nature	The bone marrow microenvironment at single-cell resolution	GSE108892
Mouse	Cpc	"MESP1, EOMES, GATA6, GATA4, ISL1, NKX2.5, HAND1, HAND2"	Cpc	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	E-cpcs	"GATA6, SOX17, HNF4A, FOXA2"	E-cpcs	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	Edothelial cells	Ramp2	Edothelial cells	Cell line	Blood	31164147	Epigenetics Chromatin	Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.	"GSE126497, GSE126501"
Mouse	Emergency granulopoietic	"Cebpb, Elane, Prtn3, Ctsg"	Emergency granulopoietic	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Emergency megakaryocytic stem-like population	"Itga2b, Pf4, Gata1, Isg15, Isg20, Stat1"	Emergency megakaryocytic stem-like population	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Gmp	"Lin-c-kit, CD16, CD32"	Gmp	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Hsc	"Lin-c-kit, Sca1, CD150"	Hsc	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Hspc-1	Ifitm1	HSPC-1	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Hspc-2	"Fos, Junb, Egr1"	HSPC-2	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Inflammatory cells	"Isg15, Ifit1, Ifit3"	Inflamed cells	Blood	Blood	32406817	eLife	Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature	GSE150166
Mouse	Lepr	Lepr	Lepr	Cell line	Blood	30971824	Nature	The bone marrow microenvironment at single-cell resolution	GSE108892
Mouse	Lsk	"Lin-c-kit, Sca1"	Lsk	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Mesoderm	"Pdgfra, Tbx6, Brachyury"	Mesoderm	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Mkp	"Lin-c-kit, CD150, CD41"	Mkp	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Mmp4	"Dntt, Cd79a, Lef1, Cd135, Cd48"	MMP4	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Mp cells	Il7r	Mp cells	Blood	Blood	32302378	The Journal of experimental medicine	Physiological expression and function of the MDR1 transporter in cytotoxic T lymphocytes	NA
Mouse	Mpp	"Lin-c-kit, Sca1"	Mpp	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Mpp2	"Lin-c-kit, Sca1, CD150, CD48"	Mpp2	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Mpp3-4	"Lin-c-kit, Sca1, CD48"	Mpp3-4	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Mural cells	Higd1b	Mural cells	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	NA	"Cd34, Mycn"	Multipotent progenitors	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527.
Mouse	NA	"Fos, Junb, Egr1"	LMPP cells	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527.
Mouse	NA	"Spi1, Ikzf1"	CLP cells	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527.
Mouse	NA	"Cdk1, Cdc20, E2f2."	Pro-B1 cells	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527.
Mouse	Lymphoid cells	"Flt3, Dntt"	Lymphoid cells	Cell line	Blood	32783885	Cell Stem Cell	Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding	"GSE144273, GSE152555"
Mouse	Neuroblasts	"Dcx, Dlx5, Gad1, Sp8"	Neuroblasts for ob-ins	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Ob immature	"Tshz1, Prokr2"	Ob immature	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Ob-in	"Gsx2, Ascl1, Dlx1, Dlx2, Gad1, Sp8, Sp9, Tshz1, Prokr2"	Ob-in	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Ob-ipcs	"Ascl1, Dlx1, Dlx2, Sp9"	Ob-ipcs	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Opcs	"Olig1, Pdgfra, Sox8, Sox10"	Opcs	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Osteogenic cells	Bglap	Osteogenic cells	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	Pluripotency cells	POU5F1	Pluripotent stem cells	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	Posterior end of the psm(presomitic mesoderm)	"Wnt , FGF"	Posterior end of the psm(presomitic mesoderm)	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Adipocytes	"Adipoq, Lepr"	Pre-adipocytes	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Adipocytes	"Cxcl12 Kitl, Fgf7, Il7"	Pre-adipocytes	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Pre-b	"Igll1, Ms4a1"	Pre-b	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Pregm	Lin-c-kit	Pregm	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Premege	"Lin-c-kit, CD150"	Premege	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Monocytes	"Csf1r, Cd36"	Pre-monocytic cells	Blood	Blood	32422235	Gene	Nascent transcript and single-cell RNA-seq analysis defines the mechanism of action of the LSD1 inhibitor INCB059872 in myeloid leukemia.	"GSE145071, GSE145106, GSE145166, GSE145211, GSE145279, GSE145410"
Mouse	Osteoblasts	"Alpl, Postn"	Pre-osteoblasts	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Osteoblasts	Clec11a14	Pre-osteoblasts	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Primary Wharton	"Procr, Fgd5, Hoxb5"	Primary Wharton	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Germ cells	"Dppa3, Ifitm3, Pou5f1, Sox2"	Primordial germ cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Proerythroblasts	"Beta-s, Hbb-b2, Tfrc, Mki67, Stmn1"	Proerythroblasts	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Granulopoietic cells	"Ltf, Pglyrp1, Lcn2, Camp, Mki67, Stmn1"	Proliferating granulopoietic cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Reticulocytes	"Cxcl12, Adipoq"	Reticulocytes	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	S1 segment of proximal tubule	"Lrp2, Slc5a12"	S1 segment of proximal tubule	Blood	Blood	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	S2 segment of proximal tubule	"Lrp2, Slc13a3"	S2 segment of proximal tubule	Blood	Blood	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Stem cells	"Itgav, Thy1, Eng, Cd200"	Skeletal stem cell	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Te cells	Klrg1	Te cells	Blood	Blood	32302378	The Journal of experimental medicine	Physiological expression and function of the MDR1 transporter in cytotoxic T lymphocytes	NA
Mouse	Tfh cells	"Batf, Cd40lg, Icos, Pdcd1"	Tfh1	Blood	Blood	31371561	Science	Identification of a T follicular helper cell subset that drives anaphylactic IgE.	GSE132798
Mouse	Tfh cells	"Il4, Il13, Gata3"	Tfh13	Blood	Blood	31371561	Science	Identification of a T follicular helper cell subset that drives anaphylactic IgE.	GSE132798
Mouse	Tri-ipcs	"Hes6, Btg2, Gsx2, Olig2"	Tri-ipcs	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Ve-cad	Cdh5	Ve-cad	Cell line	Blood	30971824	Nature	The bone marrow microenvironment at single-cell resolution	GSE108892
Mouse	Lymphocyte cells	"Tbx21, Lfng, Ccl5, Il12rb1, Gata3, Il1l1, Il5, Il13, Rorc, Il7a, Ahr, Il23r, Tbx21, Ifng, Il21r, Ccl5, Ccl4, Ccl3, Ncr1, Il15r, Eomes, Cxcr3, Il12rb1"	ILC1	Blood	Blood	28902842	Nature	The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation	GSE102299
Mouse	Lymphocyte cells	"Tbx21, Lfng, Ccl5, Il12rb1, Gata3, Il1l1, Il5, Il13, Rorc, Il7a, Ahr, Il23r, Gata3, Lmo4, Areg, Ccl1, Csf2, Il4, Il5, Il13, Cxcl2, Il9, Il1rl1, Il9r, Il17rb, Klrg1"	ILC2	Blood	Blood	28902842	Nature	The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation	GSE102299
Mouse	Lymphocyte cells	"Tbx21, Lfng, Ccl5, Il12rb1, Gata3, Il1l1, Il5, Il13, Rorc, Il7a, Ahr, Il23r, Rorc, Tcf7, Batf3, Il17f, Il17a, Il22, Ncr1, Il1r1, Ahr, Il23r, Cxcr5, Ccr6"	ILC3	Blood	Blood	28902842	Nature	The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation	GSE102299
Mouse	Endothelial cells	"Etv2, Cdh5, Pecam1"	Endothelial cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Basophils	"Prss34, Mcpt8"	Basophils	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Basophils	"Ccl3, Fcer1a, Mcpt8"	Basophils	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	"Ebf1, Pax5"	B cells	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527
Mouse	B cells	"Ebf1, Cd79b, Igll1"	Committed B-cell progenitors	Blood	Blood	29440259	Genes Dev	Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.	GSE107527.
Mouse	Erythrocytes	"Klf1, Epor, Gata1"	Erythrocytes	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Lymphocyte cells	"Dntt, Flt3, Rag2"	Lymphoid progenitors	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Mast cells	"Gzmb, Cma1"	Mast cells	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Mast cells	"Ms4a2, Fcer1a"	Mast cells	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	B cells	"CD19, GFRA2, BST1"	Early B cells	Tissue	Blood	29899037	J Exp Med	Dissection of progenitor compartments resolves developmental trajectories in B-lymphopoiesis	GSE92540
Mouse	B cells	"CD20, CD19, KIT"	LP cells	Tissue	Blood	29899037	J Exp Med	Dissection of progenitor compartments resolves developmental trajectories in B-lymphopoiesis	GSE92541
Mouse	B cells	"CD21, CD19, KIT"	Pro_B cells	Tissue	Blood	29899037	J Exp Med	Dissection of progenitor compartments resolves developmental trajectories in B-lymphopoiesis	GSE92542
Mouse	B cells	"Cd79a, Cd79b, Cd74, Cd83"	"B cells, mature"	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	B cells	"Cd79a, Cd79b, Vpreb1"	"B cells, immature"	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	B cells	"Cd79a, Cd79b, Vpreb3"	Pre-B cells	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	Natural killer (NK) cells	"Nkg7, Il2rb, Thy1"	Natural killer (NK) cells	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	T cells	Cd7	T cells	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	Cell cycling cells	"Mki67, Ccnb2, Cdc20"	Cell cycling cells	Tissue	Blood	31406379	Nat Immunol	The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation	GSE112542
Mouse	Chondrocytes	"Acan, Col2a1"	Chondrocytes	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	Chondrocytes	"Acan, Sox9"	Chondrocytes	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Chondrocytes	"lhh, Sfrp5, Anln"	Chondrocytes	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	B cells	"Dntt, Rag1, Rag2"	Early pro-b cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Granulocytes	"Ltf, Pglyrp1, Lcn2, Camp"	Granulocytes	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Granulocytes	"Ltf, Camp, Ngp, S100a11, Pglyrp1, Ccl3, Fcer1a, Mcpt8"	Basophils	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic stem cells	Lin-KitSca1	Hematopoietic stem cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	"Chchd10, Cd79a, Cd79b, Cd19, Mki67, Stmn1"	Immature B cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer (NK) cells	"Kirb1a, Kirb1b, Kirb1c, Ncr1"	Immature Natural killer (NK) cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	"Pax5, Rag1, Rag2"	Late pro-b cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	"Cd79a, Cd79b, Cd19, Ms4a1, Cd74"	Mature B cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Monocytes	"Cd68, Mpeg1, Itgam, Emr1, Fcgr3"	Monocytes	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer (NK) cells	"Kirb1a, Kirb1b, Kirb1c, Ncr1"	Natural killer (NK) cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer (NK) cells	"Mki67, Stmn1"	Pre-natural killer (NK) cell	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer (NK) cells	"Ifngr1, Cxcr4, Fxyd5, S1pr1, Clsn3, Tm2d2, Pear1, B4galt1, Emb"	Natural killer (NK) cells	Blood	Blood	30413361	Immunity	High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mouse	GSE119563
Mouse	Cycling cells	Mki67	Cycling cells	Blood	Blood	32406817	eLife	Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature	GSE150166
Mouse	T cells	"Ccl3, Cxcr6, Gzmb"	Th1 cell	Blood	Blood	30487586	Nat Commun	Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection	GSE111027
Mouse	T cells	"Cxcr5, Tcf7, Sostdc1"	Tfh cell	Blood	Blood	30487586	Nat Commun	Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection	GSE111027
Mouse	B cells	CD19	B cells	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	CD4 T cells	CD4	CD4 T cells	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	CD8 T cells	CD8	CD8 T cells	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Erythrocytes	ter119	Erythrocytes	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Granulocytes	"SSC, Gr1"	Granulocytes	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Monocytes	"SSC, CD11b"	Monocytes	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Myeloid cells	CD11b	Myeloid cells	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Dendritic cells	"Siglech, Xcr1"	Dendritic cells	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Natural killer (NK) cells	NK1.1	Natural killer (NK) cells	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Hematopoietic stem cells	Fgd5	Hematopoietic stem cells	Cell line	Blood	30561434	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	B cells	"Cd79a, Cd19, Cr2, Fcer2a, CD22, Ms4a1, CD86, H2-Ab1, Cd24a, Cd38, CD40"	B cells	Blood	Blood	30564855	Immunogenetics	The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcgammaR) in the G_ttingen minipig.	NA
Mouse	Dendritic cells	"Itgax, Thbd, Cd38, Cd209a, Cd74, Flt3, H2-Aa, H2-Eb1, Ifi30, Napsa, Itgb7, Syngr2, Clec10a, Ahr, Tlr13, CD24a"	Dendritic cells	Blood	Blood	30564855	Immunogenetics	The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcgammaR) in the G_ttingen minipig.	NA
Mouse	Monocytes	"Cd14, Cd68, Adgre1, Lgals3, Apoe, Mafb, Fcgr3, Ly6e, H2-Aa, H2-Eb1"	Monocytes	Blood	Blood	30564855	Immunogenetics	The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcgammaR) in the G_ttingen minipig.	NA
Mouse	Natural killer (NK) cells	"Ncr1, Klrb1c, Klrd1, Klrc1, Klrk1, Itga2, Gzma, Gzmb, Prf1"	Natural killer (NK) cells	Blood	Blood	30564855	Immunogenetics	The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcgammaR) in the G_ttingen minipig.	NA
Mouse	Differentiated cells	"Sox11, Neurod6, Pou3f1, Satb2"	Differentiating pyns	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Endoderm cells	"Car4, H19, Trh"	Early endoderm cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Progenitor cells	"Ly6a, Cd34, Thy1, Mfap5, Clec3b"	Early mesenchymal progenitors	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Progenitor cells	Cd34	Early progenitor cells	Cell line	Blood	31164147	Epigenetics Chromatin	Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.	"GSE126497, GSE126501"
Mouse	Ectoderm cells	"Sox1, Pax6, Pou3f1"	Ectoderm cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Ectoderm cells	"Gm2694, Mir124-2hg"	Ectoderm cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Endoderm cells	"Sox17, Epcam, Foxa1, Foxa2"	Endoderm cells	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Endoderm cells	SOX17	Endoderm cells	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	Endothelial cells	"Pecam1, Cd34, Vwf"	Endothelial progenitors	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Erythrocytes	"Gata2, Gata1, Klf1, Epor, Hba-a2"	Mature erythrocytes	Blood	Blood	30890159	Genome Biology	GAPA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells	NA
Mouse	Monocytes	"Irf8, Csf1r, Ctsg"	Monocytes	Blood	Blood	30890159	Genome Biology	GAPA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells	NA
Mouse	Eosinophils	Prss57	Eosinophils	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Eosinophils	"Prg2, Prg3"	Eosinophil progenitors	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Eosinophils	CD170	Eosinophils	Blood	Blood	32337387	J Immunol Regen Med	Single Cell Sequencing Analysis of Lizard Phagocytic Cell Populations and Their Role in Tail Regeneration	NA
Mouse	Eosinophils	SiglecF	Eosinophils	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	Epithelial cells	"SNAIL1, SNAIL2, MMP2, VIM"	Epithelial mesenchymal transition	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	Erythroblasts	"Beta-s, Hbb-b2, Bpgm"	Erythroblasts	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Progenitor cells	"Cd45, Cd71, Cd71"	Erythroid	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Endothelial cells	Cdh5	Bone marrow-derived endothelial cells (BMECS)	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	Fibroblasts	S100a4	Fibroblasts	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	Stromal cells	"Lepr, Cxcl12"	Mesenchymal stromal cells	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	Stromal cells	"Vcam1, Pdgfrb, LepR, Cdh11"	Bone marrow stromal cells	Tissue	Blood	31149730	Eur J Immunol	Single-cell transcriptomes of murine bone marrow stromal cells reveal niche-associated heterogeneity	GSE131365
Mouse	Erythrocytes	Hba-X	Erythrocytes	Cell line	Blood	31164147	Epigenetics Chromatin	Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.	"GSE126497, GSE126501"
Mouse	Megakaryocytes	Gp1bb	Megakaryocytes	Cell line	Blood	31164147	Epigenetics Chromatin	Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.	"GSE126497, GSE126501"
Mouse	Granular cells	"Flt3, Kit, Mpeg1, Itgb2, Ahnak, Pld4, Cd68"	Granulocyte monocyte progenitors	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Kit, Stmn1, Mki67, Gpr56, Cd34"	Hematopoietic precursor cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Kit, Gpr56, Cd34, Pdzk1ip1, Ly6a"	Quiescent HSC-enriched fraction	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Kit, Gpr56, Cd34, Stmn1, Mki67, Cd48, Flt3, Cd34"	HSCs__he MPPs	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Kit, Gpr56, Cd34, Tgm2, Klf1, Treml1"	Megakaryocyte erythrocyte progenitor (MEP)	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Kit, Gpr56, Cd34, Dntt, Ly6c2, Ctsg, Tyrobp, Cd69"	Common lymphocyte progenitor lineage (CLP	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hematopoietic cells	"Ly6e, Lmo2, Hoxa9, Runx1, Cd34, Gfi1, Egfl7, Myl10, Ctsg, Prtn3"	Hematopoietic stem and progenitor cells	Cell line	Blood	33302977	J Hematol Oncol	Trajectory of chemical cocktail_induced neutrophil reprogramming	NA
Mouse	Progenitor cells	"car4, Cdkn1c, Ttr"	Hepatic progenitors	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	Monocytes	"Camp, Ccl6, Ly6c2, Lgals1"	Immature monocytes	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	B cells	Vpreb3	B cells	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Dendritic cells	CD209a	Dendritic cells	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Erythrocytes	Hba-a2	Erythrocytes	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Granulocytes	Ly6g	Granulocyte	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Monocytes	Csf1r	Monocytes	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Stem cells	CD34	Stem cell	Tissue	Blood	31439836	Nat Commun	B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.	NA
Mouse	Progenitor cells	"Tnn, Ostn"	Late mesenchymal progenitors	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	CD8 T cells	NA	Exhausted CD8+ T cells	Tissue	Blood	31527834	Nat Immunol	PTPN2 regulates the generation of exhausted CD8 + T cell subpopulations and restrains tumor immunity	GSE134413
Mouse	CD8 T cells	NA	Exhausted CD8+ T cells	Tissue	Blood	31527834	Nat Immunol	PTPN2 regulates the generation of exhausted CD8 + T cell subpopulations and restrains tumor immunity	GSE134413
Mouse	CD8 T cells	NA	Exhausted CD8+ T cells	Tissue	Blood	31527834	Nat Immunol	PTPN2 regulates the generation of exhausted CD8 + T cell subpopulations and restrains tumor immunity	GSE134413
Mouse	CD8 T cells	NA	Exhausted CD8+ T cells	Tissue	Blood	31527834	Nat Immunol	PTPN2 regulates the generation of exhausted CD8 + T cell subpopulations and restrains tumor immunity	GSE134413
Mouse	CD8 T cells	NA	Exhausted CD8+ T cells	Tissue	Blood	31527834	Nat Immunol	PTPN2 regulates the generation of exhausted CD8 + T cell subpopulations and restrains tumor immunity	GSE134413
Mouse	Progenitor cells	Hey1	Lineage committed progenitors	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	B cells	Cd79a	B cells	NA	Blood	31551511	Scientific Reports	"Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component"	GSE132199
Mouse	B cells	CD79A	B cells	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Megakaryocytes	PPBP	Megakaryocytes	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Monocytes	MS4A7	Monocytes	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Monocytes	MS4A7	Monocytes	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Natural killer (NK) cells	GNLY	Natural killer (NK) cells	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Macrophages	"CD45, Adgre1, F4, F80, Lyz2"	Bone marrow_derived macrophage and adipose tissue macrophages )	Tissue	Blood	30990466	JCI Insight	Single cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases.	"GSE117176, GSE32575, GSE54350,"
Mouse	Macrophages	"Ahnak, Mpeg1, Emr1, Cd68, Ly6d, Irf8, Cd74"	Bone marrow macrophages	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	CD8 T cells	NA	CD8 T cells	Blood	Blood	31606264	Immunity	TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision	GSE131535
Mouse	CD8 T cells	NA	CD8 T cells	Blood	Blood	31606264	Immunity	TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision	GSE131535
Mouse	Macrophages	"CD45, Adgre1, F4, 80, Lyz2, Nos2, CD86, Tnf"	M1	Tissue	Blood	30990466	JCI Insight	Single cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases.	"GSE117176, GSE32575, GSE54350,"
Mouse	Macrophages	"CD45, Adgre1, F4, F80, Lyz2, Ym1, Arg1, Fizz-1, Mgl2"	M2	Tissue	Blood	30990466	JCI Insight	Single cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases.	GSE117176
Mouse	Macrophages	"Mrc1, Mrc2, Arg1, Arg2"	M2 macrophages	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Macrophages	"Adgre1, Cx3cr1, Apoe"	Macrophages	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	B cells	"Cd19, Cd79b"	B cells	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Myeloid cells	"Itgam, Cd14, Csf1r"	Myeloid cells	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Natural killer T (NKT) cells	"Cd8a, Cd4, Cd3e, Cd3g, Foxp3, Nkg7, Cd7"	Natural killer T (NKT) cells	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Macrophages	Ms4a7	Macrophages	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Macrophages	"Cd14, Ly6c2"	Maturing macrophages	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	Macrophages	NA	Macrophages	Blood	Blood	32703960	Sci Rep	Trajectory analysis quantifies transcriptional plasticity during macrophage polarization	NA
Mouse	Macrophages	NA	Macrophages	Blood	Blood	32703960	Sci Rep	Trajectory analysis quantifies transcriptional plasticity during macrophage polarization	NA
Mouse	Monocytes	"CD11b, Ly6Chi CCR2hi monocyte"	Cluster 1	Tissue	Blood	31803182	Front Immunol	Defining the Signature of VISTA on Myeloid Cell Chemokine Responsiveness.	NA
Mouse	Monocytes	"CD12b, Patrolling Ly6C_ CX3CR1hi Nr4a1 monocyte"	Cluster 2	Tissue	Blood	31803182	Front Immunol	Defining the Signature of VISTA on Myeloid Cell Chemokine Responsiveness.	NA
Mouse	Monocytes	"CD13b, MHC-II"	Clusters 3	Tissue	Blood	31803182	Front Immunol	Defining the Signature of VISTA on Myeloid Cell Chemokine Responsiveness.	NA
Mouse	Monocytes	"CD14b, MHC-II"	Clusters 5	Tissue	Blood	31803182	Front Immunol	Defining the Signature of VISTA on Myeloid Cell Chemokine Responsiveness.	NA
Mouse	Monocytes	"CD15b, IFN-I, CD209a, MHC-II"	Cluster 4	Tissue	Blood	31803182	Front Immunol	Defining the Signature of VISTA on Myeloid Cell Chemokine Responsiveness.	NA
Mouse	Monocytes	"Ahnak, Mpeg1, Emr1, Cd68"	Mature monocytes	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Monocytes	"Camp, Ccl6, Clec4d, Ly6c2"	Mature monocytes	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	Megakaryocytes	"Pf4, Itga2b, Gp1bb"	Megakaryocyte progenitors	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Progenitor cells	"Mcam, Nes, Cxcl12"	Mesenchymal progenitors	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Endothelial cells	"Cdh5, Pecam, Sca1, Ly6a"	Arterial Ecs	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Endothelial cells	"Cdh5, Pecam, Emcn"	Sinusoidal ECs	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Muscle cells	"Tagln, Acta2"	Smooth muscle cells	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Monocytes	"Irf8, Csf1r, Ly86"	Monocyte progenitors	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Progenitor cells	"Kit, Sca1, Cd150"	Multipotent progenitors (mpps)	Blood	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Myeloid cells	Lin-c-kit	Myeloid progenitors	Tissue	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Myeloid cells	Kit	Myeloid progenitors	Blood	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Myeloid cells	"Kit, Sox4, Camp, Ltf, Ly6c2, Lgals1"	Myeloid progenitors	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	T cells	"Ccr7, Lef1, Sell, Dapl1, Igfbp4"	Naive T cells	Blood	Blood	33139915	Nat Immunol	Intravenous nanoparticle vaccination generates stem-like TCF1 + neoantigen-specific CD8 + T cells	GSE158240
Mouse	B cells	Cd79a	B cells	Blood	Blood	32075963	Nat Commun	Immune checkpoint modulation enhances HIV-1 antibody induction	PRJNA556211
Mouse	CD4 T cells	Cd4	CD4 T cells	Blood	Blood	32075963	Nat Commun	Immune checkpoint modulation enhances HIV-1 antibody induction	PRJNA556211
Mouse	CD8 T cells	Cd8a	CD8 T cells	Blood	Blood	32075963	Nat Commun	Immune checkpoint modulation enhances HIV-1 antibody induction	PRJNA556211
Mouse	Neural cells	"SHH, ZEB1, ZEB2, NCAM2"	Neural differentiation	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	Neutrophils	"Ly6g, Ltf, Mmp9"	Neutrophils	Blood	Blood	31689243	JCI insight	CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis	GSE139492
Mouse	Neutrophils	"Elane, Gfi1, Cebpe"	Neutrophil progenitors	NA	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Neutrophils	"Elane, Prtn3, Mpo"	Neutrophils	Blood	Blood	29588278	Blood	A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant Mouse	"GSE106973, GSE107727"
Mouse	Neutrophils	"Mmp9, Srgn, Cxcr2"	Maturing neutrophils	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	Neutrophils	"Elane, Cepbe, Gfi1"	Neutrophils	Blood	Blood	30890159	Genome Biology	GAPA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells	NA
Mouse	Neutrophils	"Ngp, Lcn2, Lrg1, S100a8, Mmp8, Fpr1, Ltb4r"	Neutrophils	NA	Blood	31551511	Scientific Reports	"Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component"	GSE132199
Mouse	Neutrophils	"Fpr2, Orm1"	Neutrophils	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Neutrophils	S100a8	Neutrophils	Blood	Blood	32668198	Cell	The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid- Type I IFN Signaling Axis	GSE150387
Mouse	Neutrophils	"Elane, Mpo"	Neutrophils	Blood	Blood	32929473	Blood	RUNX1 and CBFbeta-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development	GSE152573
Mouse	Neutrophils	"Camp, Ltf, Ly6c2"	Immature neutrophils	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	Neutrophils	"Camp, Ccl6, Ly6c2, Lgals1, Cx3cr1, Apoe"	Mature neutrophils	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	Neutrophils	"S100a8, S100a9, Cxcr2, Csf3r, S100a9, Il1b, Tnf, Ccl3, Acod1, G0s2"	Neutrophils	Blood	Blood	32978242	Sci Immunol	The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages	GSE157244
Mouse	Neutrophils	"Mpo, Elane, Ctsg"	Neutrophils	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Oligodendrocytes	"Olig1, Olig2, Pdgfra, Sox10"	Oligodendrocytes	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	Osteoblasts	"Col1a1, Bglap, Spp1, Alpl, Postn, Tnc, Pth1r, Sox9, Runx2, Sp7, Atf4"	Osteoblasts	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Osteoblasts	Ifitm5	Osteoblasts	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Osteoblasts	Ctnnb1	Osteoblasts	Tissue	Blood	31949165	Nat Commun	A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.	"GSE136970, GSE136973, GSE136979"
Mouse	Osteoblasts	"Osteocalcin, Bglap, Col1a1"	Osteoblasts	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Osteoblasts	"Sp7, Alpl, Ibsp, Bglap, Dmp1, Alpl, Ibsp"	Osteoblast progenitors	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Osteoblasts	"Sp7, Alpl, Ibsp, Bglap, Dmp1, Sp7, Alpl"	Preosteoblasts	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Osteoblasts	"Sp7, Alpl, Ibsp, Bglap, Dmp1, Bglap, Dmp1"	Osteoblasts	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Osteoblasts	"Csf1r, Spi1, Cx3cr1, Trem2, Nfatc1"	Osteoblasts	Tissue	Blood	31934494	Bone Res	Focal adhesion protein Kindlin-2 regulates bone homeostasis in Mouse	NA
Mouse	Osteoblasts	Col22a1	Osteoblasts	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Osteoblasts	Dkk1	Osteoblasts	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Adipocytes	Ms4a4d	Adipocytes	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Erythrocytes	Slfn14	Erythrocytes	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Monocytes	Ms4a4c	Monocytes	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Natural killer (NK) cells	Klre1	Natural killer (NK) cells	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	B cells	"CD22, CD79a, CD83, JCHAIN, IGHM"	B cells	Blood	Blood	32337387	J Immunol Regen Med	Single Cell Sequencing Analysis of Lizard Phagocytic Cell Populations and Their Role in Tail Regeneration	NA
Mouse	Mast cells	CAP3	Mast cells	Blood	Blood	32337387	J Immunol Regen Med	Single Cell Sequencing Analysis of Lizard Phagocytic Cell Populations and Their Role in Tail Regeneration	NA
Mouse	Monocytes	"CD68, CTSS, LY86, CST3"	Monocytes	Blood	Blood	32337387	J Immunol Regen Med	Single Cell Sequencing Analysis of Lizard Phagocytic Cell Populations and Their Role in Tail Regeneration	NA
Mouse	T cells	"CD247, CD8b, LGALS1"	T lymphocytes	Blood	Blood	32337387	J Immunol Regen Med	Single Cell Sequencing Analysis of Lizard Phagocytic Cell Populations and Their Role in Tail Regeneration	NA
Mouse	Pericytes	Acta2	Pericytes	Tissue	Blood	31130381	Cell	A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia	NA
Mouse	T cells	"Cd3d, Cd3e, Cd3g, Ncr1, Klrb1a, Klrb1b, Klrb1c"	T cells	Blood	Blood	32406817	eLife	Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature	GSE150166
Mouse	Lymphocyte cells	"Tmem176a, Tmem176b, Cxcr6"	Innate lymphoid cells (ILCs)	Blood	Blood	32406817	eLife	Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature	GSE150166
Mouse	Natural killer (NK) cells	"Ncr1, Klrb1a, Klrb1b, Klrb1c"	Natural killer (NK) cells	Blood	Blood	32406817	eLife	Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature	GSE150166
Mouse	B cells	B220	B cells	Tissue	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Erythrocytes	"Ly6G, Mac1, Ter119, CD71"	Erythrocytes	Tissue	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Granulocytes	"Ly6G, Mac1"	Granulocytes	Tissue	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Hematopoietic stem cells	"Kit, Sca1"	Hematopoietic stem cells	Blood	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Megakaryocytes	"Kit, CD150, CD41"	Megakaryocytes	Tissue	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Monocytes	Mac1	Monocytes	Tissue	Blood	32413320	Cell	An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells	NA
Mouse	Dendritic cells	"Siglech, Ly6d"	Plasmacytoid dendritic cell progenitor	Blood	Blood	32422235	Gene	Nascent transcript and single-cell RNA-seq analysis defines the mechanism of action of the LSD1 inhibitor INCB059872 in myeloid leukemia.	"GSE145071, GSE145106, GSE145166, GSE145211, GSE145279, GSE145410"
Mouse	Plasmacytoid dentritic cells	LILRA4	Plasmacytoid dentritic cells	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	Platelet	"CD41, CD150"	Platelet	Blood	Blood	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Platelet	Hemgn	Platelet	Tissue	Blood	32286228	eLife	Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment	GSE145477
Mouse	Progenitor cells	"Cd34, Kit"	Progenitor cells	NA	Blood	29921301	Genome Biology	dropEst:pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments	GSE65525
Mouse	Monocytes	"Ahnak, Mpeg1, Mki67, Stmn1"	Proliferating promonocytes	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Glia cells	"Dbi, Aldoc, Slc1a3, Gli3"	Radial glia cells	Blood	Blood	32234482	Cell	Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog	GSE140817
Mouse	B cells	Cd79a	B cells	Blood	Blood	32668198	Cell	The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid- Type I IFN Signaling Axis	GSE150387
Mouse	Monocytes	"Csf1r, Ly6C2, Ccr2, Cx3cr1, Cd209a"	Monocytes	Blood	Blood	32668198	Cell	The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid- Type I IFN Signaling Axis	GSE150387
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Blood	Blood	32668198	Cell	The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid- Type I IFN Signaling Axis	GSE150387
Mouse	T cells	Ctla4	Regulatory T cells (Treg)	Blood	Blood	32075963	Nat Commun	Immune checkpoint modulation enhances HIV-1 antibody induction	PRJNA556211
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Blood	Blood	32515782	J Exp Med	BACH2 drives quiescence and maintenance of resting Treg cells to promote homeostasis and cancer immunosuppression	GSE128176
Mouse	Schwann cells	"Mog, Mag"	Schwann cells	Tissue	Blood	31871321	Nat Cell Biol	"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization."	GSE122467
Mouse	Schwann cells	POU5F1	Schwann cells	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	B cells	"Cd79A, Cd19"	B cells	Blood	Blood	32929473	Blood	RUNX1 and CBFbeta-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development	GSE152573
Mouse	T cells	"Cd3e, Cd4, Cd8a, Cd6"	Immature T cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	"Ahnak, Thy1, Cd3e, Cd8"	T cells	Tissue	Blood	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	"Cd3e, Cd3d, CD40, CD8a, CD8b1, CD5, Ms4a4b, Cd28, Il7r, Lef1, Dapl1, Cd3e, Cd8a, Gzmk, Gzmm, Ccl5, S100a6, Lgals1, Klrk1, Crtam, Eomes"	Cytotoxic T cells	Blood	Blood	30564855	Immunogenetics	The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcgammaR) in the G_ttingen minipig.	NA
Mouse	T cells	Cd3g	T cells	NA	Blood	31551511	Scientific Reports	"Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component"	GSE132199
Mouse	T cells	CD3E	T cells	Blood	Blood	31574155	Gigascience	IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis.	GSE60361.
Mouse	B cells	"Klf2, Zbtb32, Bach2, Il9r, Ccr6, Cd38, S1pr1"	Memory B cells	Blood	Blood	33010224	Immunity	Affinity-Restricted Memory B Cells Dominate Recall Responses to Heterologous Flaviviruses.	GSE154102
Mouse	Fibroblasts	"COL3A1, IGFBP7"	Fibroblasts	Cell line	Blood	33054971	eLife	"GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm"	NA
Mouse	T cells	Cd3d	T cells	Blood	Blood	32668198	Cell	The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid- Type I IFN Signaling Axis	GSE150387
Mouse	Erythrocytes	"Klf1, Gata1"	Erythrocytes	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Hematopoietic stem cells	Procr	Hematopoietic stem cells	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Lymphocyte cells	"Dntt, Flt3"	Lymphocytes	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Mast cells	"Gzmb, Cma3, Mcpt8"	Mast cells	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Megakaryocytes	"Itga2b, Pf4, Vwf"	Megakaryocytes	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Monocytes	"Irf8, Ms4a6c"	Monocytes	Blood	Blood	33147438	Mol Cell	Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mouse and Humans	GSE157832
Mouse	Progenitor cells	"Car4, Trh, Tagln2"	Thyroid and lung progenitors	Blood	Blood	29311656	Nat Cell Bio	Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation	NA
Mouse	B cells	"Ebf1, Bach2, Pax5, Id3"	Follicular B cells	Cell line	Blood	33302977	J Hematol Oncol	Trajectory of chemical cocktail_induced neutrophil reprogramming	NA
Mouse	B cells	CD23	Follicular naive B cells	Cell line	Blood	33302977	J Hematol Oncol	Trajectory of chemical cocktail_induced neutrophil reprogramming	NA
Mouse	Cmop	"Cd34, Ly6c2"	Cmop	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Mdp	"Cd34, Kit, Fcgr3, Ly6c2, Csf1r"	Mdp	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Meg	"Cd34, Kit"	Meg	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Mp	"Cd34, Kit, Fcgr3, Ly6c2"	Mp	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neuronal cells	"Fcgr3, Ly6c2"	Pre-neuronal cells 1	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neuronal cells	"Ly6c2, Itgam, Cd177"	Pre-neuronal cells 2	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neuronal cells	"Fcgr3, Ly6c2, Itgam, Ly6g, Cd177"	Pre-neuronal cells 3	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neural cells	"Fcgr3, Ly6c2, Vcam1"	Proneu-1	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neural cells	"Fcgr3, Ly6c2, Vcam1, Itgam"	Proneu-2	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Monocytes	"CD11b, Ly6Chi"	Classical monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	"CD11b, Ly6Chi"	Classical monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Hematopoietic cells	"Cd34, Kit"	Hematopoietic stem and progenitor cells	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Macrophages	"F4, F80"	Macrophages	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Macrophages	"Siglec1, Arg1, Mrc1, Csfr1, Tgfb1, Tgfbr1"	Macrophages	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Macrophages	"F4, F80"	Macrophages	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Macrophages	"Siglec1, Arg1, Mrc1, Csfr1, Tgfb1, Tgfbr1"	Macrophages	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	"CD11b, Ly6Clo"	Alternatively activated monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	"CD11b, Ly6G_, Ly6Clo"	Alternatively activated monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	CD11b	Monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	"Siglec1, Arg1, Mrc1, Csfr1, Tgfb1, Tgfbr1"	Monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	CD11b	Monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Monocytes	"Siglec1, Arg1, Mrc1, Csfr1, Tgfb1, Tgfbr1"	Monocytes	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Neutrophils	"CD11b, Ly6G"	Neutrophils	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Neutrophils	"CD11b, Ly6G"	Neutrophils	Tissue	Bone	32024825	Nat Commun	Regulation of heterotopic ossification by monocytes in a Mouse model of aberrant wound healing	NA
Mouse	Erythrocytes	Kit	Erythrocytes	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Neural cells	"Ly6c2, Itgam, Ly6g, Cd177"	Immature neurons	Tissue	Bone	32494068	Nature	Mouse models of neutropenia reveal progenitor-stage-specific defects	GSE120409
Mouse	Basal ganglia	"Ntn1, Slc6a3"	Basal ganglia	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Basal plate	"Fgfbp3, Spon1, Id3, Shh, Foxa2, Ntn1, Ednrb"	Basal plate	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Basal plate	"Spon1, Dmrta2, Shh, Shisa3, Sulf1, Foxa2, P4ha3, Corin, Aldh1l1, Tacr1, Ntn1, Bcas1, Sulf2, Serpine2, Slit1, Fgfbp3, Fam210b, Dok5, Lrrn1, Npl, Cdc42ep3, Cthrc1, Hpgd, Enpp2, Scrn1, Pcdh8, S100a10, Ndrg2, Pak3, E130114P18Rik, Fabp7, Rgma, Limch1, Lmx1a, H"	Basal plate	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Capillaries	"Tfrc, Car4, Slc16a1"	Capillaries	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Cartex	Satb2	Cartex	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Caudal thalamus	"Gbx2, Cd47, Rora, Id4, Chst1, Cd47, Slc18a2, Hs6st2, Epha3, Robo2, Kitl, Neurog1, Dll1"	Caudal thalamus	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Calb1, Gbx2, Sp9"	Caudal thalamus neuron I	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Crabp2, Syt13, Cd47"	Caudal thalamus neuron II	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Cerebellum	"Arap1, Pax3, Ntn1"	Cerebellum	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Claupyr	"Tbr1, Pcp4"	Claupyr	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Neural cells	"Tbr1, Pcp4"	Cortext layer5 /layer6 pyramidal	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Neural cells	"Eomes, Neurog2"	Cortical excitatory ipc	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Wnt8b, Dkk3, Rspo1"	Cortical hem	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Tlx3, Arx"	Cortical interneuron	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Neural cells	"Pax6, Vim, Nes"	Cortical retina ganglion cells (rgcs)	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Dentate gyrus granule cells	Prox1	Dentate gyrus granule cells	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Tumor cells	"Cdk1, Ccna2, Cenpf"	Dividing tumor cells	NA	Brain	32579914	Cell Rep	NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma	GSE150752
Mouse	Efferocytosis	"Rac1, Il10ra, Mfge8, Mafb, Fasl"	Efferocytosis	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Epithalamus-derived lateral habenular nucleus	Pou4f1	Epithalamus-derived lateral habenular nucleus	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	External granular layer (egl) cell	"Neurod1, Ccdn2"	External granular layer (egl) cell	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Gaba intermediate cells (gaba int)	"Pax2, Lhx5"	Gaba intermediate cells (gaba int)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Gabaergic	Tal1	Gabaergic	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Gabaergic and glutamatergic	"Gad1, Tal1, FoxP1, Vsx2, Nkx6-1"	Gabaergic and glutamatergic	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Ghrh_th	"Plcb4, Prkar2b, Adcy1"	Ghrh_th	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Glioblastoma multiforme	IL4R	Glioblastoma multiforme	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Glutamatergic	Vsx2	Glutamatergic	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Glutamatergic cerebellar nuclei early (glucn early)	"Atoh1, Meis2, Lhx9"	Glutamatergic cerebellar nuclei early (glucn early)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Glutamatergic cerebellar nuclei late (glucn late)	"Lmx1a, Meis2"	Glutamatergic cerebellar nuclei late (glucn late)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Glutamatergic cerebellar nuclei mid (glucn mid)	"Meis2, Lhx10"	Glutamatergic cerebellar nuclei mid (glucn mid)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Hemoglobin-expressing vascular cells	"Cldn5, Cldn5"	Hemoglobin-expressing vascular cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Hippocampal pyramidal - crym	Crym	Hippocampal pyramidal - crym	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Hippocampal pyramidal precursor	Nrp1	Hippocampal pyramidal precursor	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Hippocampus	"Fn1, Tspan18"	Hippocampus	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Homoeostatic	"P2ry12, Tmem119, Trem2"	Homoeostatic	Tissue	Brain	33054973	eLife	A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult Mouse brain	GSE150169
Mouse	Hypendymal cells	"Ccdc153, Sspo, Rax, Ttr"	Hypendymal cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Igl-dcn	"Pnoc, Snhg11, Tcf7l2, Gad1, Gad2, Lhx9"	Igl-dcn	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Immature gc	Fxyd7	Immature gc	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Inflammasome-il-1b pathway	"Il1b, Nlrp3, Nlrc4"	Inflammasome-il-1b pathway	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Jakstat signaling	"Jak1, Stat1"	Jakstat signaling	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Low quality cells	"Hb-a1a, Hbb-y, Hbb-bs"	Low quality cells	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Mature gc	"Plk5, Ntng"	Mature gc	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Medial ganglionic eminences	Nkx2-1	Medial ganglionic eminences	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Medulia	"Pax2 , Ntn1"	Medulia	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Meningeal cells	Cxcl12	Meningeal cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Meningeal cells	Cxcl12	Meningeal cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Meningeal cells	Foxc1	Meningeal cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Stem cells	Prrx2	Mesenchymal stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Stem cells	Prrx2	Mesenchymal stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Microglia homeostatic	"Fcrls, Cx3cr1, Tmem119, P2ry12"	Microglia homeostatic	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Migrating interneuron	"Dlx1, Dlx2, Dlx5, Dlx6, Lhx6, Foxp2, Adarb2"	Migrating interneuron	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Microglia cells	"Apoe, C1qb, Fcer1g"	Microglia cells	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Mirgrating interneuron	Dlx6os1	Mirgrating interneuron	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Neural cells	"Vacht, Olig2"	Motor neuron	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Mural cells	"Kcnj8, Abcc9, Mustn1, Mhy11"	Mural cells	Cell line	Brain	31447324	Cell Metab	Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	NA
Mouse	Mural cells	Vtn	Mural cells	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Myelomonocytic cells	"Ccr2, Mrc1, Lyz2, Cd163"	Myelomonocytic cells	Organoids	Brain	30850344	Immunity	Microglial Function Is Distinct in Different Anatomical Locations during Retinal Homeostasis and Degeneration	"GSE126783, GSE33089, GSE126783."
Mouse	NA	"Arx, Maf"	Precursor state 1	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	NA	"Isl1, Ebf1"	Precursor state 1	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	NA	"Retnla, Clec10a, Folr2, Timd4, Mrc1"	SnMac2	Tissue	Brain	32284604	Nat Neurosci	"Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury"	NA
Mouse	Microglia cells	"Apoe, Ctsb"	Neurodegeneration-related microglia	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Microglia cells	"Isg15, Ifit3"	Interferon-related microglia	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Macrophages	Mrc1	Perivascular macrophages	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Microglia cells	"Top2a, Mki67"	Proliferating microglia	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Myeloid cells	"S100a6, Msrb1"	"Neutrophils, Monocytes"	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Neurogenic cells	Mki67	Proliferating cells	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neurogenic cells	"Ascl1, Dlx2"	Neural progenitors	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neurogenic cells	"Sox4, Sox11"	Neurogenic and Neural differentiation	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neuts	"S100a9, S100a8, Camp, Ly6g"	Neuts	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Neural cells	Gbx2	Newborn neuron precursors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Nlpc	"Mxd3, Ascl1, Neurog2, Rfc4, Lockd"	Nlpc	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Noradrenergic cells	"Tfap2b, Phox2b"	Noradrenergic cells	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Noradrenergic cells	"Hand2, Dbh"	Noradrenergic cells	Cell line	Brain	31315047	Cell Rep	Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons	GSE132184
Mouse	Noradrenergic cells	"Stmn3, Syn2, Dbh, Snap 25, Cyb561, Tubb3"	Noradrenergic neuronal cells	Cell line	Brain	31315047	Cell Rep	Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons	GSE132184
Mouse	Npcs	"Tfap2b, Ccnd2"	Npcs	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Oec	Mybpc1	Oec	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Olfactory bulb	Deptor	Olfactory bulb	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Glia cells	"Npy, Gja1"	Olfactory ensheathing glia	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Oligodendrocytes	Mbp	Oligodendrocytes	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Oligodendrocytes	Pdgfra	Oligodendrocytes	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Oligodendrocytes	"Mog, Cnp, Plp1, Mbp"	Oligodendrocyte-like cells	Tissue	Brain	31539496	Cell	"Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements"	"GSE117154, GSE131675, GSE131672, GSE131940, GSE131873"
Mouse	Opcs	"Olig2, Pdgfra"	Opcs	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Opcs	"Pdgfra, Vcan"	Opcs	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Opcs	Olig1	Opcs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Opcs	Pdgfra	Opcs	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Germ cells	Prox1	Pan germ cells	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Hematopoietic cells	Ptprc	Pan hematopoietic	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Neuronal cells	"Tuj1, Stmn2, Stmn3"	Pan neuronal cells	Cell line	Brain	31315047	Cell Rep	Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons	GSE132184
Mouse	Schwann cells	"Erbb3, S100b, Mbp, Plp1"	MySCs	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Schwann cells	"Erbb3, S100b, Ngfr, p75"	NmSCs	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Neuronal cells	"Grin1, Rbfox3"	Pan-neuronal cells	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Pc early	"Foxp2, Lhx5"	Pc early	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Pc late	"Calb1, Foxp2"	Pc late	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Perivascular cells	"Apoe, Cc74, Mrc1"	Perivascular mf	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Post-capillary venules	"Nr2f2, Flt4, Vwf"	Post-capillary venules	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Projection neuron	"Isl1, Ebf1"	Projection neuron	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Purkinje cells	"Pcp4, Gad1, Gad2"	Purkinje cells	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Purkinje cells	Calb1	Purkinje cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Purkinje cells	Calb1	Purkinje cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Rmtg	"Sox14, FoxP1, Sox2"	Rmtg	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Roof plate	"Ttr, Rspo3, Ezr"	Roof plate	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Roof plate	"Bmp4, Msx1, Trpm3, Mab21l2, Clic6, Fgf8, Rspo2, 4931429I11Rik, Esm1, Wnt1, Calml4, Lypd6, Car14, Rbp4, Bmp7, Ifitm2, Klhdc8b, Klk8, Fibcd1, Cbln1, Tmem108, Galnt12, Wnt9a, Sfrp1, Nrn1, Ezr, Sepp1, Mdk, Kcna5, Slit2, Igfbp7, Sostdc1, Serpinh1, Vtn, Alcam"	Roof plate	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Stem cells	"Lmx1a, Msx1, Bmp7"	Roof plate like stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Stem cells	"Lmx1a, Msx1, Bmp7"	Roof plate like stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Rostral midbrain	Tfap2d	Rostral midbrain	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Neural cells	"Bhlhe23, Neurog1, Neurod1"	Rostral pretectal neuronal precursor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"ISlr2, Bhlhe23, Ntm"	Rostral pretectal nuerons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rostral pretectum	"C1ql2, Bhlhe23, Irx2, Islr2, Lmo3, Ebf3"	Rostral pretectum	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rostral pretectum	"Tmsb4x, Igfbpl1, Ptn, Rspo1, Barhl2, Ccnd1, Cd24a, Olig3, Rspo3, 2810417H13Rik, Rrm2, Anp32b, Dut, Fabp5, Akr1b3, Macrod2, Shox2, Cdca7, Dctpp1, Pcna, Neurog2, Cenpw, Fgf15, Prim1, Fkbp4, Dnajc9, Dek, 2310009B15Rik, Mcm5, Nasp, Pdlim1, Neurog1, Rfc4, Flrt"	Rostral pretectum	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rostral thalamic neuronal precursor	"Tal2, Pnoc, Gata2"	Rostral thalamic neuronal precursor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rostral thalamus	"Sox14, Gata3, Gata2, Tal1"	Rostral thalamus	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rostral thalamus/prethalamus	"Pdlim3, Nkx2-2, Gsx1, Gsx2, Helt, Ckb, Olig2, Nnat, Nkx2-9, Dlx2, Tubb2a, Olig1, Ptch1, Sox21, Slc25a5, Emx2, Fam181b, Lhfp, Dlk1, Itm2a, Peg10, Arl4a, Fst, Gpm6a, Acot1, Gpm6b, Ntn1, Shh, Tubb2b, Dll3, Arx, 2510009E07Rik, Kiz, Serpine2, Cdk5r1, Ascl1, Ed"	Rostral thalamus/prethalamus	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Rv2 precursor	"Lhx4, Vsx2, Skor1, Sox14"	Rv2 precursor	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	S1pyrdl	"Pcp4, Tbr1"	S1pyrdl	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Serotonergic precursors	"Gata2, Gata3"	Serotonergic precursors	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Snmacs	"CD206, Mgl2"	Snmacs	Tissue	Brain	32284604	Nat Neurosci	"Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury"	NA
Mouse	Spinal motor	"Vacht , Olig2"	Spinal motor	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Spinalcord	Pdella	Spinalcord	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Striatal	Gpr88	Striatal	Tissue	Brain	32637622	Sci Adv	Molecular atlas of the adult mouse brain	GSE147747
Mouse	Striatum	Rarb	Striatum	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Tanycytes	"Gja1, Rax"	Tanycytes	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Taste cells	KRT8	Taste cells	Tissue	Brain	32259485	Cell	Defining the Design Principles of Skin Epidermis Postnatal Growth	GSE145216
Mouse	Thalamic	Rora	Thalamic	Tissue	Brain	32637622	Sci Adv	Molecular atlas of the adult mouse brain	GSE147747
Mouse	Thalamic precursors	"Olig3, Barhl2"	Thalamic precursors	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Thalamus	"Syt13, Chst1, Shisa9, Cd47, Robo2, Prokr2, Id4, Elmo1, Wif1, Ntng1, Pou2f2, Tmem132a, Kitl, Rora, Hs6st2, Pdzm3, Crabp2, Dmrtb1, Slc18a2, Enpp2"	Thalamus	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Thalamus	Fign	Thalamus	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Tight junction	Cldn5	Tight junction	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Unipolar brush cells (ubc)	Eomes	Unipolar brush cells (ubc)	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Unipolar brush cells (ubc)	Eomes	Unipolar brush cells (ubc)	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Unipolar brush cells (ubc)	"Pax6, Eomes"	Unipolar brush cells (ubc)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Unipolar brush cells of the dorsal cochlear nucleus	"Eomes, Lmx1a, Calb2"	Unipolar brush cells of the dorsal cochlear nucleus	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Unipolar brush cells_granule neuron intermediate cells (ubc/gn int)	Pax6	Unipolar brush cells_granule neuron intermediate cells (ubc/gn int)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Upper rhombic lip early (url early)	"Wnt1, Lmx1a"	Upper rhombic lip early (url early)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Upper rhombic lip late (url late)	"Wnt1, Otx2, Pax6, Sla1a3"	Upper rhombic lip late (url late)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Vascular leptomeningeal cells	"Il33, Ptgds"	Vascular leptomeningeal cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Vascular leptomeningeal cells	"Lum, Pdgfra"	Vascular leptomeningeal cells	Cell line	Brain	31447324	Cell Metab	Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	NA
Mouse	Vascular leptomeningeal cells	"Pdgfra, Gja1, Slc6a13"	Vascular leptomeningeal cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Vascular leptomeningeal cells	Slc6a13	Vascular leptomeningeal cells	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Vascular leptomeningeal cells	Rgs5	Vascular leptomeningeal cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Vasculature	"P2ry14, Notch3"	Vasculature	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Ventral forebrain rgc	"Nes, Nkx2-1, Ascl1, Rbp1"	Ventral forebrain rgc	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Vsx2 glutamatergic	"Lhx4, Skor1, Shox2, Sox14"	Vsx2 glutamatergic	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Zone limitans intrathalamica	"Pitx2, Dmrta2, Nr4a2, Foxa2"	Zone limitans intrathalamica	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Apical progenitors	Id3	Apical progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Astrocyte-like cells	"Agp4, Gfap, Apoe, Id3"	Astrocyte-like cells	Tissue	Brain	31539496	Cell	"Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements"	"GSE117154, GSE131675, GSE131672, GSE131940, GSE131873"
Mouse	Astrocytes	Aldoc	Astrocytes	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Astrocytes	"Sox9, Etv4, Sall3, Grin2c, Kcng4"	Astrocytes	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Microglia cells	C1qc	Microglia cells	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Neural cells	Stmn2	Neurons	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Oligodendrocytes	Mog	Oligodendrocytes	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Glial cells	Gdf10	Bergmann glia cells	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Neural cells	"Reln, Mpped1, Id2"	E18.5 id2 neurons	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Neural cells	"Vip, Synpr, Igf1"	E18.5 vip neurons	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Neural cells	"Sst, Tspan7, Satb1"	Early stage pvalb neurons	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Neural cells	"Mef2c, Erbb4, Plcxd3"	Early stage sst neurons	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Endothelial cells	"Igfbp7, Col4a1"	Endothelial cells	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Neural cells	Neurod6	Excitatory neurons	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Blood cells	"Hbb-bs, Hba-a1"	Blood cells	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Blood cells	CD31	Blood cells	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Progenitor cells	Olig3	Brainstem progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Progenitor cells	Olig3	Brainstem progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	"Nppb, N31ra, Etv1"	Neural cells c11	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Mrgpra3, Etv1"	Neural cells c12	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Trpm8, foxp2, gpr26"	Neural cells c1-2	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Mrgprd, Grik1, Trpc3"	Neural cells c13	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Cd34, Cdh9, Gm7271"	Neural cells c3	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"S100b, Pcdh7, Ntng1, Rgs6, Piezo2"	Neural cells c4	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Ntrk2, Cacna11, Scn5a"	Neural cells c5	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"S100b, Scn10a, Calca, Htr3a, Piezo2"	Neural cells c6	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Neural cells	"Trpv1, Trpa1, Tac1, Calca"	Neural cells c7-10	Tissue	Brain	31592768	eLife	Stereotyped transcriptomic transformation of somatosensory neurons in response to injury	GSE131272
Mouse	Cajal-Retzius cells	"Reln, Lhx1, Lhx5"	Cajal-Retzius cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Cajal-Retzius cells	"Trp73, Reln"	Cajal-Retzius cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Progenitor cells	"Rrm2, Spc25, Hmgb2"	Caudal thalamic intemediate progenitor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Progenitor cells	"Ptn, Id3, Rspo1"	Caudal thalamic neural progenitor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Arachnoid barrier cells	"Abcg2, Pgp"	Arachnoid barrier cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Endothelial cells	Bmx	Arterial endothelial cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Astrocytes	Aldoc	Astrocytes	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Endothelial cells	Meox1	Capillary endothelial cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Neural cells	Npy	Neurons	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Oligodendrocytes	"Plp1, Sox10"	Oligodendrocytes	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Endothelial cells	Slc38a5	Venous endothelial cells	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Cell cycling cells	"Hmgb2, Top2a, mKi67"	Cell cycling cells	Tissue	Brain	31539496	Cell	"Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements"	"GSE117154, GSE131675, GSE131672, GSE131940, GSE131873"
Mouse	Progenitor cells	Mki67	Cerebellar interneuron progenitor	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Choroid plexus cells	NA	Choroid plexus cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Choroid plexus cells	"Lcn2, 1500015O10Rik"	Choroid plexus cells	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Choroid plexus cells	Ttr	Choroid plexus cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Brain	30269986	Neuron	PDGFRb Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2	GSE112436
Mouse	Endothelial cells	Lyve1	Lymphatic vessel endothelial cells	Tissue	Brain	30269986	Neuron	PDGFRb Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2	GSE112436
Mouse	Microglia cells	"Iba1, Aif1"	Microglia cells	Tissue	Brain	30269986	Neuron	PDGFRb Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2	GSE112436
Mouse	Muscle cells	Acta2	Smooth muscle cells	Tissue	Brain	30269986	Neuron	PDGFRb Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2	GSE112436
Mouse	Arterioles	"Bmx, Jag1, Efnb2"	Arterioles	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Aldh1l1, Slc1a3, Aqp4, Gdf10, Vim, Nbl1, A2m"	Bergman glia	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Aldh1l1, Slc1a3, Aqp4, Slc17a7, Neurod6, Mab21l1"	Excitatory neurons	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Aldh1l1, Slc1a3, Aqp4, Gad1, Reln, Calb1"	Inhibitory neurons	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Aldh1l1, Slc1a3, Aqp4, Dcx, Dlx2, Ascl1, Hes5"	Neuroprogenitor cells	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Aldh1l1, Slc1a3, Aqp4, Des, Mcam, Pdgfrb"	Pericytes	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	"Pecam1, Cldn5, Slco1c1, Ocln"	Biliary epithelial cells	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Oligodendrocytes	"Mog, Mag, Gjc2"	Mature myelinating oligodendrocytes	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Microglia cells	"Cx3cr1, P2ry12, Tmem119, MHC-II"	Microglia cells	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Oligodendrocytes	"Pdgfra, Susd5, Cspg4"	Oligodendrocyte progenitors	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Astrocytes	"Clu, Apoe"	Astrocytes	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Neural cells	Atoh1	Atoh1 neuronal progenitors	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Endothelial cells	Egfl7	Endothelial cells	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Microglia cells	"C1qa, C1qb, C1qc, Tmem119"	Microglia cells	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Oligodendrocytes	"Pdgfra, Olig1, Olig2"	Oligodendrocyte precursors	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Corticotropes	Rasgrf2	Corticotropes	Tissue	Brain	32637622	Sci Adv	Molecular atlas of the adult mouse brain	GSE147747
Mouse	Cycling cells	Top2a	Cycling cells	Tissue	Brain	31659342	Nat Neurosci	Stem-cell-derived human microglia transplanted in mouse brain to study human disease	GSE137444
Mouse	Cycling progenitors	"Top2a, Ube2c, Mki67, Hmgb2, Cenpf;"	Cycling progenitors	Tissue	Brain	32973039	Genome Res	Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain	GSE142274
Mouse	Microglia cells	"Fcrls, P2ry12, Cx3cr1, Trem2, C1qa, Tubb3, Meg3, Dcx."	Microglia cells	Tissue	Brain	30471926	Immunity	Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes	GSE98971
Mouse	Microglia cells	"Fcrls, P2ry12, Cx3cr1, Trem2, C1qa, Gfap"	Microglia cells	Tissue	Brain	30471926	Immunity	Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes	GSE98971
Mouse	Microglia cells	"Fcrls, P2ry12, Cx3cr1, Trem2, C1qa, Olig1"	Microglia cells	Tissue	Brain	30471926	Immunity	Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes	GSE98971
Mouse	Microglia cells	"Fcrls, P2ry12, Cx3cr1, Trem2, C1qa, Vtn"	Microglia cells	Tissue	Brain	30471926	Immunity	Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes	GSE98971
Mouse	Astrocytes	"Acsbg1, Aldh1, Glast, S100beta, Vimentin"	Astrocytes	Tissue	Brain	30624206	eLife	eIF2B activator prevents neurological defects caused by a chronic integrated stress response.	GSE18617
Mouse	Neural cells	"Calbindin-1, KCC2"	Neurons	Tissue	Brain	30624206	eLife	eIF2B activator prevents neurological defects caused by a chronic integrated stress response.	GSE18617
Mouse	Oligodendrocytes	"Mbp, Coronin1A"	Oligodendrocytes and microglia	Tissue	Brain	30624206	eLife	eIF2B activator prevents neurological defects caused by a chronic integrated stress response.	GSE18617
Mouse	Differentiated cells	"Cntn2, Pax6, NeuroD1, Tubb3, Gap43"	Differentiated cells	NA	Brain	32579914	Cell Rep	NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma	GSE150752
Mouse	Differentiated cells	Rora	Differentiating purkinje cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Differentiated cells	Rora	Differentiating purkinje cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Endothelial cells	"Pdgfrb, Pecam1"	Endothelial cells	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Neural cells	NA	Atoh1	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Neural cells	NA	"Neurod1, Reln, Nhlh1, Rbfox3"	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Neural cells	NA	"Pcp2, Calb1, Sema3a, Shh, Rora, Gad1"	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Neural cells	NA	"Gad1, Pax2, Ptf1a"	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Myeloid cells	"Spi1, Ly6e, Ccl9, Hmgb1, Ccr2, Irf8"	Monocytes/macrophages	Tissue	Brain	30728335	JCI Insight	Cxcr4-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Neural cells	"Gadd45g, St18, Btg2, Tis21"	Early neuronal precursors	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Myeloid cells	"Spil, Hmgb1, ly6θ, Crc2, CcL9, Lrf8"	Monocytes/macrophages	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Neural cells	"Map2, Slit2, Scn1a, Scn8a"	Somatosensory neurons 1	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Neural cells	"Cckar, Th, Kif5c, Gabre1"	Somatosensory neurons 2	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Endothelial cells	"Hes1, Hes5, Lhx1, Lhx5, Atoh1, Barhi1, Cldn5, Vtn"	Endothelial cells_pericytes_erythrocytes	Tissue	Brain	30735127	eLife	Specification of diverse cell types during early neurogenesis of the Mouse cerebellum	GSE120372
Mouse	Neural cells	"Lhx1, Lhx5"	Gabaergic neurons	Tissue	Brain	30735127	eLife	Specification of diverse cell types during early neurogenesis of the Mouse cerebellum	GSE120372
Mouse	Neural cells	"Atoh1, Barhl1"	Glutamatergic neurons	Tissue	Brain	30735127	eLife	Specification of diverse cell types during early neurogenesis of the Mouse cerebellum	GSE120372
Mouse	Microglia cells	"P2ry12, Siglech, Sparc"	Microglia cells	Organoids	Brain	30850344	Immunity	Microglial Function Is Distinct in Different Anatomical Locations during Retinal Homeostasis and Degeneration	"GSE126783, GSE33089, GSE126783."
Mouse	Myeloid cells	"Ccr2, Mrc1, Lyz2"	Myeloid cells	Organoids	Brain	30850344	Immunity	Microglial Function Is Distinct in Different Anatomical Locations during Retinal Homeostasis and Degeneration	"GSE126783, GSE33089, GSE126783."
Mouse	Endothelial cells	"Vtn, Lgals1, Col3a1"	Endothelial cells	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"ISlr2, Tac1, Necab2, Tac1, Pou4f1, Lmo3, Nefm, Irx1, Irx3, Irx2, Ebf3, Cntn2"	Epithalamic neurons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Stmn2, Gap43"	Postmitotic neurons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	Hs6st2	Postmitotic neurons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Dlx5, Dlx2, Dlx1, Gad2, Gad1, Arx"	Prethalamic neurons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Npy, Gata3, Sox14"	Rostral thalamus neurons	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Ependymal cells	"Foxj1, Wdr52"	Ependymal cells	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Ependymal cells	Foxj1	Ependymal cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Ependymal cells	Dnah11	Ependymal cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Ependymal cells	"Foxj1, S100b"	Ependymal cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Ependymal cells	Sema3c	Ependymal cells	Tissue	Brain	32973039	Genome Res	Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain	GSE142274
Mouse	Ependymal cells	Rarres2	Ependymal cells	Tissue	Brain	33037292	Commun Biol	Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography	NA
Mouse	Ependymal cells	"Ccdc153, Hdc"	Ependymal cells	Cell line	Brain	31447324	Cell Metab	Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	NA
Mouse	Ependymal cells	"Gja1, Ccdc153"	Ependymal cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Astrocytes	"Slc1a3, Aldh1l1"	Astrocytes	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Neural cells	Dlx1	Gabaergic neurons	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Neural cells	Neurod1	Glutamatergic neurons	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Oligodendrocytes	"Olig1, Olig2"	Oligodendrocytes	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Astrocytes	Gdf10	Astrocytes/bergmann glia	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Astrocytes	Aldh1l1	Astrocytes/bergmann glial precursors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	Pax2	GABA interneurons	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	Pax2	GABA interneurons	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Microglia cells	Alf1	Microglia cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Microglia cells	Alf1	Microglia cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Oligodendrocytes	Mobp	Myelinating oligodendrocytes	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Oligodendrocytes	Mobp	Myelinating oligodendrocytes	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Oligodendrocytes	"Olig1, Pdgfra"	Oligodendrocyte precursors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Oligodendrocytes	"Olig1, Pdgfra"	Oligodendrocyte precursors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	"Lhx2, Lhx9"	Post mitotic ntz neurons	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	"Lhx2, Lhx9"	Post mitotic ntz neurons	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Fibroblasts-like cells	Igfbp2	Fibroblasts-like cells	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Neural cells	"Ret, Ntrk1"	Sensory neurons	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Neural cells	"Dlx1, Dlx2"	Forebrain inhibitory neuron progenitors	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Progenitor cells	Ptf1a	Gaba progenitors 1	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Progenitor cells	Lhx5	Gaba progenitors 2	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Neural cells	"Tuj1, Map2"	General neuron	Cell line	Brain	32523990	Sci Adv	Generation of self-organized sensory ganglion organoids and retinal ganglion cells from fibroblasts.	PRJNA597624
Mouse	Neural cells	"Tubb3, Map2."	Generic neuronal	Cell line	Brain	31086315	Nat Neurosci	Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.	GSE114176
Mouse	Astrocytes	"Aqp4, Aldoc, Gfap, Fabp7"	Astrocytes	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Oligodendrocytes	"Olig1, S100b"	Oligodendrocyte	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Microglia cells	"Ptprc, Aif1"	Microglia	Tissue	Brain	30690467	J Mol Cell Biol	Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum	GSE122357
Mouse	Progenitor cells	Fabp7	Gliogenic progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Progenitor cells	Fabp7	Gliogenic progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	Adora2a	ISPN	Tissue	Brain	31178122	Cell	Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity	NA
Mouse	Neural cells	Drd1	DSPN	Tissue	Brain	31178122	Cell	Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity	NA
Mouse	Neural cells	"Tshz1, Otof, Cacng5"	ESPN	Tissue	Brain	31178122	Cell	"YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury"	NA
Mouse	Granular cells	Atoh1	Granule neuron progenitors	Tissue	Brain	32294450	Cell Rep	Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2 + Granule Neuron Precursor	GSE118068
Mouse	Granular cells	Pax6	Granule neuron progenitors	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Granular cells	"Atoh1, Zic1,Mcm6, Srebf1, Ung"	GNP_G1	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Granular cells	"Atoh1, Zic2, Dek, Top2a, Hist1h1t"	GNP_S	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Granular cells	"Atoh1, Zic3, Ccnb2, Cdc20, Cenpa"	GNP_G2M	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Granular cells	"Atoh1, Zic4, Rbfox3, Neurod1, Tubb3"	GNP_mature	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Granular cells	"Lhx5, Skor1, Tfa2b"	Granule neuron progenitors	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Hepatocytes	Apoa2	Hepatocytes	Organoids	Brain	32955435	eLife	Genetic mapping of etiologic brain cell types for obesity	"GSE74672, GSE87544, GSE113576, GSE93374, GSE125065, GSE109774, SRP135960"
Mouse	Granular cells	Prox1	Hippocampal granule	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Granular cells	"Prox1, Nrp2"	Hippocampal granule precursor	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Microglia cells	P2RY12	Homeostatic microglial	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Microglia cells	"Fcrls, P2ry12, Cx3xr1"	Homeostatic microglial	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Fibroblasts	"Col1a2, Col1a1, Dcn, Fn1"	Fibroblasts	Cell line	Brain	31315047	Cell Rep	Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons	GSE132184
Mouse	Astrocytes	"Hes5, Sla1a3"	Astrocytes	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Neural cells	Pax6	Granule neurons	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Glial cells	Mki67	Intermediate glial progenitor cells	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Progenitor cells	Neurog1	Intermediate progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Progenitor cells	"Eomes, Neurod1, Gadd45g, Sstr1"	Intermediate progenitors	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Microglia cells	"P2RY12, P2RY13, CX3CR1, TMEM119, CD9, TREM2, LPL, ITGAX"	Disease-associated microglia	Tissue	Brain	31375314	Neuron	Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo	GSE133436
Mouse	Macrophages	"Ifit3, Isg15"	Activated macrophages	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Neural cells	"Snap25, Syt1"	Neurons	Cell line	Brain	31447324	Cell Metab	Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	NA
Mouse	Oligodendrocytes	"Mal, Klk6"	Oligodendrocytes	Cell line	Brain	31447324	Cell Metab	Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	NA
Mouse	Astrocytes	"Aqp4, S100b, Slc1a3"	Astrocytes	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Neural cells	"Hoxa2, Mroh2a, Hoxb2"	Glutamatergic neurons	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Immune cells	"Cx3cr1, C1qb, C1qa"	Immune cells	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Oligodendrocytes	"Olig1, Lhfpl3, Sox10"	Oligodendrocytes	NA	Brain	31474569	Cancer Cell	Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse	GSE120974
Mouse	Leukocytes	PTPRC	Leukocytes	Organoids	Brain	30827680	Cell	Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain	GSE115626
Mouse	Oligodendrocytes	"Ccnd2, Olig1, Meg3"	Oligodendrocyte progenitors	Tissue	Brain	31539496	Cell	"Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements"	"GSE117154, GSE131675, GSE131672, GSE131940, GSE131873"
Mouse	Arachnoid barrier cells	"Slc6a13, Gja1, Slc47a1"	Arachnoid barrier cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Dendritic cells	Cd209a	Dendritic cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Neural cells	Sox11	Immature neurons	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Microglia cells	Tmem119	Microglia cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Monocytes	"Cd44, Plac8"	Monocytes	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Oligodendrocytes	Pdgfra	Oligodendrocyte precursors	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Oligodendrocytes	Cldn11	Oligodendrocytes	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Muscle cells	"Cldn5, Acta2"	Vascular smooth muscle cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Macrophages	"Apoe, Nfkbia, Itgax, Axl"	Inflammatory macrophages	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Macrophages	"C3, C1pc, Cxcl13, Ccl2, Apoe, Cd9"	Inflammatory macrophages	Tissue	Brain	32209470	Cell Rep	Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System.	GSE145708
Mouse	Macrophages	Il1b	Inflammatory macrophages	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Astrocytes	Clu	Astrocytes	Tissue	Brain	31659342	Nat Neurosci	Stem-cell-derived human microglia transplanted in mouse brain to study human disease	GSE137444
Mouse	Monocytes	Ccr2	Monocytes	Tissue	Brain	31659342	Nat Neurosci	Stem-cell-derived human microglia transplanted in mouse brain to study human disease	GSE137444
Mouse	Neural cells	Npy	Neurons	Tissue	Brain	31659342	Nat Neurosci	Stem-cell-derived human microglia transplanted in mouse brain to study human disease	GSE137444
Mouse	Macrophages	Pf4	Macrophages	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Macrophages	"Mrc1, F13a1"	Macrophages	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Astrocytes	Apoe	Astrocytes	Tissue	Brain	31695190	Nat Struct Mol Biol	An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome	NA
Mouse	Neural cells	"Snap25, Neurod6, Gad1"	Gabaergic neurons	Tissue	Brain	31695190	Nat Struct Mol Biol	An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome	NA
Mouse	Neural cells	"Snap25, Neurod6, Gad1"	Glutamatergic neurons	Tissue	Brain	31695190	Nat Struct Mol Biol	An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome	NA
Mouse	Microglia cells	C1qb	Microglia cells	Tissue	Brain	31695190	Nat Struct Mol Biol	An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome	NA
Mouse	Oligodendrocytes	Mog	Oligodendrocytes	Tissue	Brain	31695190	Nat Struct Mol Biol	An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome	NA
Mouse	Macrophages	"Il4ra, Il10ra, Stat3, Stat6"	M2-like macrophages	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Macrophages	"Itgal, F10, Gda"	Macrophages	Tissue	Brain	31902528	Neuron	TREM2 Regulates Microglial Cholesterol Metabolism upon Chronic Phagocytic Challenge	GSE130627
Mouse	Macrophages	"CD64, F4, F80, CD45"	Macrophages	Tissue	Brain	32284604	Nat Neurosci	"Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury"	NA
Mouse	Macrophages	Cd68	Macrophages	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Macrophages	"Cd163, Cx3cr1, P2ry12, Tmem119"	Non-parenchymal macrophages	Tissue	Brain	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	"Cd163, Cd206, Mrc1"	Perivascular macrophage	Tissue	Brain	30269986	Neuron	PDGFRb Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2	GSE112436
Mouse	Macrophages	Cd163	Perivascular macrophage	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Astrocytes	"Aldoc, Gfap, Aqp4, Slc1a3"	Astrocytes	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Slc17a6, Tbr1, Bhlhe22, Bhlhb5"	Cortical excitatory neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Endothelial cells	"Tie1, Tek, Vwf"	Endothelial cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Erythrocytes	Hba-a1	Erythrocytes	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Macrophages	"Ms4a6d, Cybb, Tgfbi, Slamf7, Isg20, Smox, Apoe, Ms4a7"	Macrophages	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Neural cells	"Dlx1, Dlx2, Lhx6"	Forebrain inhibitory neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Gad2, Dlx5, Dlx6"	Forebrain inhibitory neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Macrophages	Lyz2	Macrophages	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Microglia cells	"Hexb, Ly86"	Microglia cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Oligodendrocytes	"Fyn, Mbp, Mog, Mal, Plp1"	Oligodendrocytes	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Atoh1, Olig3, Pcsk9, Barhl1"	Pontine mossy fiber neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	"Gpr88, Foxp1"	Striatal medium spiny neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Neural cells	Gbx2	Thalamic neurons	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Muscle cells	Acta2	Vascular smooth muscle cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Astrocytes	Aldoc	Astrocytes	Tissue	Brain	31780669	Nat Commun	Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets	NA
Mouse	Endothelial cells	Cdh5	Endothelial cells	Tissue	Brain	31780669	Nat Commun	Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets	NA
Mouse	Neural cells	Tbr1	Excitatory neurons	Tissue	Brain	31780669	Nat Commun	Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets	NA
Mouse	Neural cells	Gad1	Inhibitory neurons	Tissue	Brain	31780669	Nat Commun	Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets	NA
Mouse	Oligodendrocytes	Olig1	Oligodendrocytes	Tissue	Brain	31780669	Nat Commun	Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets	NA
Mouse	Macrophages	"Trem2, C1qa"	TREM2-hi macrophage	NA	Brain	32336197	Circ Res	Regulatory T Cells License Macrophage Pro-Resolving Functions During Atherosclerosis Regression	NA
Mouse	Microglia cells	"Cx3cr1, Tmem119"	Microglia cells	Tissue	Brain	31902528	Neuron	TREM2 Regulates Microglial Cholesterol Metabolism upon Chronic Phagocytic Challenge	GSE130627
Mouse	Astrocytes	"Aqp4, Gja1"	Astrocytes	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Endothelial cells	"Vtn, Itm2a"	Endothelial cells	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Neural cells	"Slc17a7, Satb2, Col5a1, Sdk2"	Excitatory neurons	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Neural cells	"Gad1, Gad2, Tac1, Penk, Sst, Npy"	Inhibitory neurons	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Microglia cells	"C1qa, Csf1r"	Microglia cells	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	Oligodendrocytes	"Mog, Cldn11"	Oligodendrocytes	Tissue	Brain	31932797	Nat Med	Human and Mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer disease.	GSE140511
Mouse	T cells	NA	Naive T cells	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Neural cells	"Id3, Ptn"	Neural progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	Nes	Neural stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	Nes	Neural stem cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	"Thbs4, Gja1"	Neural stem cells	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Neural cells	"Nestin, Olig2"	Neural stem cells	Tissue	Brain	32294450	Cell Rep	Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2 + Granule Neuron Precursor	GSE118068
Mouse	Neural cells	"Nestin, Vimentin, Prom1, Thbs4"	Neural stem cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Neuroblasts	"Eomes, Neurod4, Slc17a6, Mpped1, Calb2"	Neuroblast 1	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Neuroblasts	"Sox11, Bhlhe22, Neurod2, Gal, Igfbpl1"	Neuroblast 2	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Neuroblasts	"Sox10, Csf1r, Vtn, Tac1, Penk"	Neuroblasts	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Neuroblasts	"Gad1, Gad2, Dlx1, Dlx2, Sp8"	Neuroblasts	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Neural cells	"Scn11a, Ret, App, Trpv2, Dync1h1"	Neuron (n-1)	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Neural cells	"Sncg, Synpr, Ngfrap1, Prph, Nrn1"	Neuron (n-2)	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Neural cells	"Camk2a, Auts2, Dcx, Nyap1, Fus"	Neuron morphogenesis	Tissue	Brain	30728335	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Neural cells	"Camk2a, Nyap1, Auts2, Fus, Dcx"	Neuron morphogenesis	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Neural cells	"Gadd45g, Hes6"	Neuron progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Homer2, Tubb3"	Neuronal cells	Cell line	Brain	31315047	Cell Rep	Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons	GSE132184
Mouse	Neural cells	"Scn11a, App, Dync1h1, Ret, Trpv2"	Neuronal cells 1	Tissue	Brain	30728335	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Neural cells	"Sncg, Ngfrap1, Nrn1, Synpr, Prph"	Neuronal cells 2	Tissue	Brain	30728335	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Neural cells	"Sox11, Stmn2"	Neuronal precursors	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Neural cells	Dlx1	Neuronal progenitors and precursors derived from the ganglionic eminences	Tissue	Brain	29513653	Nature	Developmental diversification of cortical inhibitory interneurons	GSE104158
Mouse	Neural cells	"Id3, Rpl32, Cdk4, Nes, Sox2"	Neuronal stem cells	Tissue	Brain	29746837	Cell Host Microbe	An Immunocompetent Mouse Model of Zika Virus Infection.	GSE112711
Mouse	Neural cells	"Cdk1, Sox11"	Neuronal-restrictedprecursors	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Astrocytes	Aqp4	Astrocytes	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Endothelial cells	Flt1	Endothelial cells	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Neural cells	Slc17a7	Excitatory neurons	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Neural cells	Gad1	Inhibitory neurons	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Microglia cells	Apbb1ip	Microglia cells	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Oligodendrocytes	Mog	Oligodendrocytes	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Neutrophils	"Cd44, S100a9"	Neutrophils	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Neutrophils	Ccrl2	Neutrophils	Tissue	Brain	31659342	Nat Neurosci	Stem-cell-derived human microglia transplanted in mouse brain to study human disease	GSE137444
Mouse	Astrocytes	Aqp4	Astrocytes	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Endothelial cells	Flt2	Endothelial cells	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	NA	Glutamatergic neurons	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Chat, Npy"	Interneurons	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Microglia cells	Cx3cr1	Microglia cells	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Sp9, Ppp1r1b, Drd1, Drd2"	Spiny projection neurons	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Drd1, Tac1, Foxp2"	DSPNs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Drd2, Penk"	ISPNs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Casz1"	ESPNs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Sox4"	ImSPNs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Drd2, Drd1, Tac1"	DdSPNs	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Neural cells	"Foxp2, Ppp1r1b"	Mature SPN	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Progenitor cells	"Gadd45g, Hes6"	Newly committed progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Astrocytes	"Cldn10, Gfap"	Astrocytes	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Endothelial cells	"Cldn5, Acvrl1"	Endothelial cells	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Neural cells	"Neu4, Dcx"	Immature neurons	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Microglia cells	"C1qa, Trem2"	Microglia cells	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Neural cells	"Lhx5, Syt1"	Neurons	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Oligodendrocytes	"Mag, Opalin"	Oligodendrocytes	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Astrocytes	"Scl6a11, Ntsr2"	Astrocytes	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Endothelial cells	"Itm2a49, Flt1"	Endothelial cells	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Neural cells	"Syt1, Snap25"	Excitatory neurons	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Neural cells	"Npy51, Nr2f2"	Gabaergic neurons	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Microglia cells	"P2ry12, C1qa, Cx3cr1"	Microglia cells	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Oligodendrocytes	"Opc, Pdgfralpha, Olig2"	Oligodendrocyte progenitors	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Oligodendrocytes	"Cldn11, Cnp"	Oligodendrocytes	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Oligodendrocytes	"Pdgfra, Ppp1r14b, Ascl1, Btg2, Hes6"	Pri-OPCs	Tissue	Brain	30982771	Cell Stem Cell	Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis	GSE122871
Mouse	Neural cells	"Vglut2, Prph, Tubb3, Nefl, Uchl1, Phox2b, Prdm12."	Sensory neurons	Tissue	Brain	32259485	Cell	Defining the Design Principles of Skin Epidermis Postnatal Growth	GSE145216
Mouse	Progenitor cells	"Lxn, Cpe, Pax3, Fgfbp3, Wnt7b, Lmo1, Hes5, Nrarp, Vcam1, Vim, Nell2, Ednrb, Irx3, Ttyh1, Fgfr3, Pgpep1, Sall3, Fam181a, Sox9, Dlk1, Fabp7, Ppp1r1a, Pmp22, Irx5, Rgma, Slc25a5, Tcf7l2, E130114P18Rik, Meis1, Ptx3, Adora2b, Tal2, Epha3, Acss1, Cdh4, Ephb1, U"	P2 progenitors	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	B cells	Cd79	B cells	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Endothelial cells	"Cldn1, Slc16a1"	Blood nerve barrier endothelial cellss	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Fibroblasts	"Fn1, Fgfr1, Col1a, Col3a"	Fibroblasts	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Endothelial cells	"Lyve1, Prox1"	Lymphatic endothelial cells (LECs)	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Myeloid cells	Lyz2	Myeloid cells	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Endothelial cells	"Cldn5, Egfl7, Pecam1"	Vascular endothelial cells	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Muscle cells	"Acta2, Tagln, Tpm2"	Vascular smooth muscle cells	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Pericytes	Vtn	Pericytes	Tissue	Brain	30096314	Cell	Molecular Architecture of the Mouse Nervous System	NA
Mouse	Pericytes	Rgs5	Pericytes	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Pericytes	Rgs5	Pericytes	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Pericytes	"Cldn5, Kcnj8"	Pericytes	Tissue	Brain	31551601	NAT NEUROSCI	Single-cell transcriptomic profiling of the aging Mouse brain	GSE129788
Mouse	Pericytes	Kcnj8	Pericytes	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Pericytes	Pdgfrb	Pericytes	Tissue	Brain	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Pericytes	"Rgs5, Pdgrfb"	Pericytes	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Progenitor cells	"Ascl1, Dlx2"	Progenitor cells	Tissue	Brain	32130906	Cell Rep	Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development.	GSE125290
Mouse	Progenitor cells	Hes5	Progenitor cells	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Natural killer (NK) cells	"CD45, NK1.1, DX5, Cstb, Ctsc"	NK1AD	Tissue	Brain	32503894	The Journal of Immunology	Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model	GSE142853
Mouse	Natural killer (NK) cells	"CD45, NK1.1, DX5, Ctsc, Ctsd, Ccl3, Ccl4"	NK1a	Tissue	Brain	32503894	The Journal of Immunology	Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model	GSE142853
Mouse	Natural killer (NK) cells	"CD45, NK1.1, DX5, Ctsc, Ctsd, Ccl3, Ccl4"	NK1b	Tissue	Brain	32503894	The Journal of Immunology	Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model	GSE142853
Mouse	Natural killer (NK) cells	"CD45, NK1.1, DX5, Xcl1"	NK2	Tissue	Brain	32503894	The Journal of Immunology	Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model	GSE142853
Mouse	Astrocytes	"Fgfr3, Prkacb, Plce1, Pomc"	Astrocytes 1	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Astrocytes	"Mapk3, Pomc"	Astrocytes 2	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Astrocytes	Prkar2a	Astrocytes 3	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Endothelial cells	"Pde3a, Pomc"	Endothelial cells	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Microglia cells	"Prkar2b, Pik3r2"	Microglia cells	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Oligodendrocytes	"Pik3r3, Gab1, Fgfr1, Fgfr2, Plcb1, Agrp, Pomc"	Oligodendrocytes 1	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Oligodendrocytes	Pik3ca	Oligodendrocytes 2	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Oligodendrocytes	"Gab2, Akt1, Prkar2b, Map2k2, Pik3r1, Pomc, Jak2, Pik3r2"	Oligodendrocytes 3	Tissue	Brain	32507042	Hypertension	Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity	NA
Mouse	Fibroblasts	"Col1a1, Twist2"	Fibroblasts	Cell line	Brain	32523990	Sci Adv	Generation of self-organized sensory ganglion organoids and retinal ganglion cells from fibroblasts.	PRJNA597624
Mouse	Neural cells	CGRP	Peptidergic nociceptive neurons	Cell line	Brain	32523990	Sci Adv	Generation of self-organized sensory ganglion organoids and retinal ganglion cells from fibroblasts.	PRJNA597624
Mouse	Neural cells	"Trpv2, TrkC, Brn3a"	Sensory neurons	Cell line	Brain	32523990	Sci Adv	Generation of self-organized sensory ganglion organoids and retinal ganglion cells from fibroblasts.	PRJNA597624
Mouse	Astrocytes	"Gfap, Fabp7, Slc1a3"	Astrocytes	NA	Brain	32579914	Cell Rep	NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma	GSE150752
Mouse	Microglia cells	"Aif1, Cx3cr1, Adgre1"	Microglia cells	NA	Brain	32579914	Cell Rep	NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma	GSE150752
Mouse	Oligodendrocytes	"Cspg4, Pdgfra, Cntn1"	Oligodendrocytes	NA	Brain	32579914	Cell Rep	NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma	GSE150752
Mouse	Neural cells	Ptf1a	Ptf1a neuronal progenitors	Tissue	Brain	30320766	Nat Biotechnol	Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells	PRJNA428979
Mouse	Astrocytes	GFAP	Astrocytes	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	"Gad2, PV"	Interneurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Microglia cells	"Il1rl1, Tmem119, CD11b, CD45"	Microglia cells	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	NeuN	Neurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Oligodendrocytes	Olig2	Oligodendrocytes	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	Dcx	Progenitor_immature neurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	Socs2	Pyramidal neurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	Satb2	Pyramidal neurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Neural cells	Sv2b	Pyramidal neurons	Organoids	Brain	32615087	Cell	Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity	GSE150714
Mouse	Glia cells	"Brn3a, Brn3b, Isl1, Thy1.2, Sncg, Math5, Rbpms, RPF-1"	Radial glia cells	Cell line	Brain	32523990	Sci Adv	Generation of self-organized sensory ganglion organoids and retinal ganglion cells from fibroblasts.	PRJNA597624
Mouse	Astrocytes	Aldh1l1	Astrocytes	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Astrocytes	"Gfap, Aldh1l1"	Astrocytes	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Glia cells	"Tfap2c, Hopx, Rhcg, Vnn1, Wnt8b"	Radial glia-like cells	Tissue	Brain	29335606	Nat Neurosci	Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing	GSE95753
Mouse	Endothelial cells	"Flt1, Kdr"	Endothelial cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Red cells	Hbb-bs	Red blood cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Red cells	Hbb-bs	Red blood cells	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Immune cells	Dock2	Immune cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Microglia cells	"C1qb, Tgfbr1"	Microglia cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Oligodendrocytes	"Olig1, Olig2"	Oligodendrocyte precursors	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	Muscle cells	"Abcc9, Pdgfrb"	Smooth muscle cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	NA
Mouse	T cells	"CD69, ST2"	Residency T cell	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Granulocytes	S100a9	Granulocytes	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Microglia cells	"Cxc3r1, P2ry12, Tmem119"	Microglia cells	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Monocytes	S100a4	Monocytes	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	Astrocytes	"Slc1a3, Gfap, Clu"	Astrocytes	Tissue	Brain	32702314	Cell	Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer Disease	GSE152506
Mouse	Microglia cells	"Itgam, Cx3cr1, Csf1r"	Microglia cells	Tissue	Brain	32702314	Cell	Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer Disease	GSE152506
Mouse	Neural cells	Syp	Neurons	Tissue	Brain	32702314	Cell	Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer Disease	GSE152506
Mouse	Oligodendrocytes	Plp1	Oligodendrocytes	Tissue	Brain	32702314	Cell	Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer Disease	GSE152506
Mouse	Astrocytes	"Gfap, Id3"	Astrocytes	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Astrocytes	Chrdl1	Astrocytes	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Astrocytes	AC1	Astrocytes	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Astrocytes	"Il33, Id3"	Astrocytes	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Astrocytes	AC2	Astrocytes	Tissue	Brain	32758425	Cell Stem Cell	A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury	GSE139842
Mouse	Neural cells	"Lxn, Hes5, Nrarp"	Rostral pretectal neural progenitor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Neural cells	"Pdlim3, Helt, Fst"	Rostral thalamic neuronal progenitor	Organoids	Brain	30872278	Development	Defining developmental diversification of diencephalon neurons through single cell gene expression profiling	GSE122012
Mouse	Astrocytes	"S100b, Agt"	Astrocytes	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Neural cells	"Neurod2, Tbr1, Satb2"	Cortical excitatory neurons	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Endothelial cells	"Pecam1, Plvap, Esam"	Endothelial cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Oligodendrocytes	"Sox10, Olig1, Mbp, Enpp6, Mag"	Immature oligodendrocytes	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Immune cells	"Aif1, Cx3cr1"	Immune cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Oligodendrocytes	"Sox10, Olig1, Mbp, Mog, Mag"	Mature oligodendrocytes	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Oligodendrocytes	"Pdgfra, Sox10, Olig2"	Oligodendrocyte precursors	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Amplifying cells	"Egfr, Ascl1, Dlx1, Dlx2"	Transit amplifying cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Mesenchymal cells	"Pdgfrb, Myh11, Mylk"	Vasculature-associated mesenchymal cells	Tissue	Brain	32783944	Cell Rep	Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis.	GSE152281
Mouse	Schwann cells	NA	Schwann cells	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Schwann cells	NA	Schwann cells	NA	Brain	30728355	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in Mouse	"GSE122999, GSE122730"
Mouse	Schwann cells	Mpz	Schwann cells	Tissue	Brain	31768071	Nature Genetics	Stalled developmental programs at the root of pediatric brain tumors	GSE133531
Mouse	Microglia cells	CD11b	Microglia cells	Tissue	Brain	32795415	Cell	Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPbeta in Microglia.	GSE145454
Mouse	Schwann cells	"Gap43, Tac1, Bdnf"	Schwann cells 1	Tissue	Brain	30728335	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Schwann cells	"Plp1, Fabp7, Vim, Qk, Cryab"	Schwann cells 2	Tissue	Brain	30728335	JCI Insight	Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice.	GSE122730
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Sncaip, Alpl, Alox12, B4galnt1, Glul, Syt15, Tpgs2, Fam198b, Antxr1, Eml1, Gm609, Rnf144a, Stom, Prdx4, Aig1, Arhgef25, Stc1, Plat, Peak1, Tec, Efnb2, Fbxo7, Unc5b, Tpst1, Hey1, Cpm, Hrct1, Unc119b, Hbegf, Tbxa2r, Spry4, Scube2, Plcb1, Hlx, Arl15, Tsc22d1, Filip1, A430090L17Rik, Plk2, Slc36a1"	AEC1	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Egr1, Mgst1, St8sia2, Entpd1, Zbp1, Cables2, Cthrc1, Msx1, St8sia6, Cbr3, Irf6, Lcat, Olfml2a, Slc27a3, Col18a1, Fchsd2, Prkcd, Ifitm3, Mmrn2, Gata2, Fos, Marcks, Edn1, Kdm6b, Eps8l2, P2ry2, Pfkfb3, Snx10, Ssfa2, Crispld1, Prr13, Atl2, Galk1, Kazald1, Dsp, Sncg, Rasd1, Nebl, Gadd45b, Lama3, Bmx"	AEC2	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Dll4, Rasgrp3, Akr1c14, Slc25a33, Smarca2, Ets2, Rcan2, Sema6d, Gja1, Enpp2, Angpt2, Col4a3, Prdm1, Cdc42ep3, Hdac9, Pde4b, Arhgap18, Bcl2, Htra3, Gpr85, Cyp2d22, Itga4, Trak2, Nrp1, Camk2n1, Nid2, Lrrn3, Plekhh2, Rgcc, Stra6, Rgl1, Pcx, Slc1a1, Osgin1, Klhl6, Cxcl12, Spry1"	CapEC	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Nrp2, Frmd5, Tmem98, Pnkd, Atp8a1, Tmem37, Stx3, Pak1, Pitpnm2, Car14, Jak3, Tspan17, Serpinb9, Unc13c, Fcgrt, Pglyrp1, Kcp, Slc40a1, Slc38a3, Ctla2b, Tmtc2, Irf5, Nos2, Rell1, Hcn2, Coro2b, Baiap2, Rab4a, Pfkl, Trib2, Prr5l, Tmsb10, Ndnf, Car4, Slc38a5, Fmo2, Cebpd, St6gal1, AU021092, Pcdh19"	VcapEC	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Dixdc1, Nr2f2, Lbp, Adk, Ltc4s, Tspan9, Tcea3, Ndufa8, Lrrc8b, Chn2, Prcp, Icam1, Il1r1, Tbc1d2b, Nckap5, Gm7694, Bst1, Sdk1, Lcn2, Fmo1, Ctsc, Gpr182, Gm5127, Cysltr1, Hspb8, Prpf40b, Rp1, Mxra8, Prdm5, Itga3, Hs3st1, Anxa2, Golm1, Homer3, Atp1b1, Nampt, Prrt4, Sytl2, Gjc1, Actn1, Klk8, Ddah1"	VEC	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Endothelial cells	"Cldn5, Flt1, Pecam1, and Cdh5, Tmem176b, Tgtp1, Id2, Ptn, Gngt2, Tpd52l1, Frem2, Hyal2, Ifi27l2a, Tln2, Slc6a6, Car7, Vcam1, Klf4, Rfk, P2ry1, S100a10, Ehd1, Plec, S100a11, Pla2g4a, Cd9, Pdgfa, Ntn1, Thbd, C530008M17Rik, Aldh1a3, Kcnb1, Tnfrsf11a, Klf10, Carhsp1, Aldh1a1, Wnt5a, Icosl, Cfb, Myof, Adh1, Epha4, Tgm2, Slfn2"	AvEC	Tissue	Brain	32887883	Nat Commun	Pharmacologically reversible zonation-dependent Endothelial cells transcriptomic changes with neurodegenerative disease associations in the aged brain	GSE147693
Mouse	Alpha cells	Gcg	Alpha cells	Organoids	Brain	32955435	eLife	Genetic mapping of etiologic brain cell types for obesity	"GSE74672, GSE87544, GSE113576, GSE93374, GSE125065, GSE109774, SRP135960"
Mouse	Neural cells	Agrp	Mediobasal hypothalamic agouti related peptide-expressing neurons	Organoids	Brain	32955435	eLife	Genetic mapping of etiologic brain cell types for obesity	"GSE74672, GSE87544, GSE113576, GSE93374, GSE125065, GSE109774, SRP135960"
Mouse	Neural cells	Drds	Pancreatic medium spiny neurons	Organoids	Brain	32955435	eLife	Genetic mapping of etiologic brain cell types for obesity	"GSE74672, GSE87544, GSE113576, GSE93374, GSE125065, GSE109774, SRP135960"
Mouse	Neural cells	"Slc17a7, Slc17a6, Nrn1, Neurod1, Neurod2"	Excitatory neurons	Tissue	Brain	32973039	Genome Res	Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain	GSE142274
Mouse	Neural cells	"Dcx, Gad1, Gad2, Dlx6, Dlx1, Dlx5, Dlx2"	Inhibitory neurons	Tissue	Brain	32973039	Genome Res	Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain	GSE142274
Mouse	Oligodendrocytes	Akap7	Oligodendrocytes	Tissue	Brain	32973039	Genome Res	Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain	GSE142274
Mouse	T cells	"Ptprc, Cd3e"	T cells	Cell line	Brain	31548728	Nature Biotechnology	In vivo CRISPR screening in CD8 T cells with AAV_Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma	RJNA553676
Mouse	B cells	"Cd79a, Iglc3, Ms4a1, Cd19, Jchain1"	B cells	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Dendritic cells	"H2-ab1, Ifitm1, Cd86, Siglech, Klk1, Cd300c"	Dendritic cells	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Microglia cells	"Cd81, Tmem119, Sparc, P2ry12, Ccl2, Ccl7"	Microglia cells	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Monocytes	"F13a1, Hp, Gsr, Cd300a"	Monocytes	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Natural killer (NK) cells	"Ncr1, Klrb1c, Klre1, Xcl1, Bcl2"	Natural killer (NK) cells	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Astrocytes	Slc1a2	Astrocytes	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Endothelial cells	Cldn5	Endothelial cells	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Neural cells	"Pde10a, Elavl2"	Interneurons	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Microglia cells	Hexb	Microglia cells	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Neural cells	Pde10a	Neurons	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Oligodendrocytes	Vcan	Oligodendrocyte progenitors	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	Oligodendrocytes	Plp2	Oligodendrocytes	Organoids	Brain	32999463	Nature	Negative feedback control of neuronal activity by microglia	GSE149897
Mouse	T cells	"Ccl5, Cd2"	T cells	Tissue	Brain	32181251	Front Cell Dev Biol	Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro	GSE140793
Mouse	Astrocytes	"Mlc1, Slc1a3, Aldh1l1"	Astrocytes	Tissue	Brain	33031376	PLoS One	Isolation and transcriptional characterization of Mouse perivascular astrocytes	NA
Mouse	Endothelial cells	Cldn5	Vascular/endothelial cells	Tissue	Brain	33031376	PLoS One	Isolation and transcriptional characterization of Mouse perivascular astrocytes	NA
Mouse	T cells	Cd3e	T cells	Tissue	Brain	32295886	Proc Natl Acad Sci U S A	Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.	GSE142541
Mouse	Neural cells	Prox1	Dentate granule neurons	Tissue	Brain	33037292	Commun Biol	Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography	NA
Mouse	Neural cells	Wfs1	Pyramidal neurons	Tissue	Brain	33037292	Commun Biol	Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography	NA
Mouse	Neural cells	Pax7	Alar-platederived neurons	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Neural cells	"Gad1, Tal1, Gata3"	Gabaergic neurons	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Neural cells	Pitx2	Tal1-independent gabaergic neurons	Tissue	Brain	33053343	Cell Rep	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain	GSE157964
Mouse	Microglia cells	IBA1	Microglia cells	Tissue	Brain	33054973	eLife	A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult Mouse brain	GSE150169
Mouse	Myeloid cells	"Cd11b, Cx3cr1, Csf1r"	Myeloid cells	Tissue	Brain	33054973	eLife	A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult Mouse brain	GSE150169
Mouse	Astrocytes	Ntsr2	Astrocytes	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Endothelial cells	Slco1c1	Endothelial cells	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Astrocytes	Ucma	Lamina terminalis astrocytes	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Microglia cells	Fcer1g for	Microglia cells	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Neural cells	Ndrg4	Neurons	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Oligodendrocytes	Mag	Oligodendrocytes	Tissue	Brain	33057193	Nature	The cellular basis of distinct thirst modalities	GSE154048
Mouse	Astrocytes	"Aldh1l1, Aldoc, Slc1a2, Gja1"	Astrocytes	Organoids	Brain	33086039	Neuron	Context-Specifific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable	GSE156628
Mouse	Endothelial cells	"Esam, Icam2, Apold1, Nostrin"	Endothelial cells	Organoids	Brain	33086039	Neuron	Context-Specifific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable	GSE156628
Mouse	Microglia cells	"Cd68, Ptprc, Ccl3, Tnf"	Microglia cells	Organoids	Brain	33086039	Neuron	Context-Specifific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable	GSE156628
Mouse	Neural cells	"Rbfox3, Gabra1, Kcnq2, Cntn3"	Neurons	Organoids	Brain	33086039	Neuron	Context-Specifific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable	GSE156628
Mouse	Oligodendrocytes	"Mog, Sox10, Mobp, Gjc2"	Oligodendrocytes	Organoids	Brain	33086039	Neuron	Context-Specifific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable	GSE156628
Mouse	T cells	"Ctla-4, Icos"	Activated T cells	Tissue	Brain	32702313	Cell	Microglia Require CD4 T Cells to Complete the Fetalto-Adult Transition	GSE144038
Mouse	CD8 T cells	"Prf1, Lag3, Pdcd1, Havcr2"	CD8 T cells	Tissue	Brain	33113353	Cell	Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors	GSE134285
Mouse	T cells	"Cd3e, Cd4, Cd8a, Lat, Pdcd1, Gzmb"	T cells	Organoids	Brain	32999036	J Virol	Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus	NA
Mouse	Neural cells	"Pax6, Atoh1"	Unipolar brush cells/granule neuron progenitors (ubc/gn pro)	Tissue	Brain	31341285	Nature	Resolving medulloblastoma cellular architecture by single-cell genomics	GSE119926
Mouse	Vascular cells	"Myl9, Mgp"	Vascular cells	Tissue	Brain	32221280	Nat Commun	Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric Mouse brain	GSE129178
Mouse	Vascular cells	Col1a2	Vascular cells	Tissue	Brain	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE110823
Mouse	Progenitor cells	"Hes1, Hex5"	Vz neural progenitor cells (npcs)	Tissue	Brain	30735127	eLife	Specification of diverse cell types during early neurogenesis of the Mouse cerebellum	GSE120372
Mouse	Progenitor cells	Ptf1a	Vz progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Progenitor cells	Ptf1a	Vz progenitors	Tissue	Brain	31043743	Nature	Childhood cerebellar tumours mirror conserved fetal transcriptional programs	GSE118068
Mouse	Neural cells	"Camk4, Th, Vip"	Interneurons	Tissue	Brain	33420488	Science	Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to Human prostate cancer progression.	NA
Mouse	Pluripotency cells	"CD44, CD24, ALDH-1, SOX2, OCT4, NANOG"	Pluripotency cells	Cell line	Breast	31308046	Cancer Res	SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence	"GSE124888, GSE124887"
Mouse	Proliferating cells	"Ki67, PCNA"	Proliferating cells	Cell line	Breast	31308046	Cancer Res	SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence	"GSE124888, GSE124887"
Mouse	Quiescent cells	"HES1, TP53, BMP2, MKI67, TGFBR3, WNT10A"	Quiescent cells	Cell line	Breast	31308046	Cancer Res	SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence	"GSE124888, GSE124887"
Mouse	Set domain_containing protein 4-defined quiescent breast cancer stem cells	"SETD4, ANGPTL4, CA9"	Set domain_containing protein 4-defined quiescent breast cancer stem cells	Cell line	Breast	31308046	Cancer Res	SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence	"GSE124888, GSE124887"
Mouse	T cells	"Cxcr5, Cd154, Cd40l, Pdcd1, Maf, Il21"	T follicular helper cells (T fh)	Tissue	Breast	31730857	Cell	B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer	GSE136206
Mouse	Tumor cells	Epcam	Tumor cells	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Tumor cells	"Krt7, Krt18, Ccnd1, Epcam"	Breast tumors 4T1	Tissue	Breast	32117236	Front Immunol	Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.	NA
Mouse	Cancer stem cells	"Id3, Gpc3, Thy1, Sox10, Krt6"	Cancer stem cells	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Cancer stem cells	"SETD4, Ki67, CD133"	Cancer stem cells	Cell line	Breast	31308046	Cancer Res	SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence	"GSE124888, GSE124887"
Mouse	Fibroblasts	"Pdpn, Pdgfrb"	Cancer associated fibroblasts (CAFS)	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Endothelial cells	"Cd34, Pecam1"	Endothelial cells	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Natural killer (NK) cells	"Ptprc, Ncr1"	Natural killer (NK) cells	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	T cells	"Eomes, Pdcd1, Ctla4, Lag3, Tim3"	Cytotoxic T cells	Tissue	Breast	31730857	Cell	B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer	GSE136207
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Breast	31152164	Nat Genet	High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer.	GSE117309
Mouse	Fibroblasts	"Col12a1, Efemp1"	Fibroblasts	Tissue	Breast	31152164	Nat Genet	High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer.	GSE117309
Mouse	Myeloid cells	"Adgre1, Mrc1"	Myeloid cells	Tissue	Breast	31541031	SCIENCE IMMUNOLOGY	Myeloid cell_synthesized coagulation factor X dampens antitumor immunity	NA
Mouse	Macrophages	"Ptprc, Cd68"	Macrophages	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	B cells	"CD19, CD20, Pax5, Jxhain, Ly6d"	B cells	NA	Breast	31611701	Nat Immunol	Multiplexed activation of endogenous genes by CRISPRa elicits potent anti-tumor immunity	GSE133983
Mouse	Dendritic cells	"Ly75, Batf3, Clec10a, CD209A"	Dendritic cells	NA	Breast	31611701	Nat Immunol	Multiplexed activation of endogenous genes by CRISPRa elicits potent anti-tumor immunity	GSE133983
Mouse	Macrophages	Ms4a7	Macrophages	Tissue	Breast	31152164	Nat Genet	High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer.	GSE117309
Mouse	Macrophages	"CD14, Fcgr1, Adgre1"	Macrophages	NA	Breast	31611701	Nat Immunol	Multiplexed activation of endogenous genes by CRISPRa elicits potent anti-tumor immunity	GSE133983
Mouse	Macrophages	"Itgam, Adgrd1, Csf1r, Msr1"	Macrophages	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	Progenitor cells	Krt6	Mammary progenitors	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Epithelial cells	"Krt18, Epcam, Dsp"	Epithelial cells	Tissue	Breast	31881983	Breast Cancer Research	S100a4 upregulation in Pik3caH1047R;Trp53R270H;MMTV-Cre-driven mammary tumors promotes metastasis	GSE126351.
Mouse	Myeloid cells	"CD11b, Itgam"	Myeloid cells	Tissue	Breast	31881983	Breast Cancer Research	S100a4 upregulation in Pik3caH1047R;Trp53R270H;MMTV-Cre-driven mammary tumors promotes metastasis	GSE126351.
Mouse	Neutrophils	"Ptprc, Csf3r"	Neutrophils	Cell line	Breast	30042390	Nat Commun	Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer	PRJNA369574
Mouse	Fibroblasts	"Col1a1, Col3a1, Dcn, Postn"	Fibroblasts	Tissue	Breast	32117236	Front Immunol	Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.	NA
Mouse	Myeloid cells	"Ly6g, Retnlg, Cd14, Cd68"	Ly6g+Cd68+ myeloid cells	Tissue	Breast	32117236	Front Immunol	Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.	NA
Mouse	Myeloid cells	"Adgre1, Mrc1, C1qa, Fcgr2b"	F4/80+Cd68+ myeloid cells	Tissue	Breast	32117236	Front Immunol	Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.	NA
Mouse	B cells	"Cd19, Cd79a, Cd79b, Ebf1"	B cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	CD4 T cells	"Cd4, Icos, Cd3d"	CD4 T cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	CD8 T cells	"Cd3g, Cd8a, Gzmb, Cd8b1"	CD8 T cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	Mast cells	"Mcpt8, Cd200r3, Gata2, Cpa3"	Mast cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	Natural killer (NK) cells	"Klra3, Nkg7, Gzma, Ncr1"	Natural killer (NK) cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	Pericytes	"Rgs5, Mcam"	Pericytes	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Plasmacytoid dentritic cells	"Itgax, Ccr9, Siglech"	Plasmacytoid dentritic cells	Tissue	Breast	32188939	Nature	A bioorthogonal system reveals antitumour immune function of pyroptosis.	"Genomics Data Center (NGDC) under accession number PRJCA002149 , (https"
Mouse	Fibroblasts	"s Acta2, Ly6c1, Cdk1, Cd74, Crabp1, Cd53"	Cancer associated fibroblasts (CAFS)	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Endothelial cells	"Pecam1, Mcam"	Endothelial cells	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Epithelial cells	Epcam	Epithelial cells	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Fibroblasts	"Pdgfra, Dcn, Col1a1"	Fibroblasts	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Immune cells	Ptprc	Immune cells	PDX	Breast	32455670	Cancers (Basel)	Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer	NA
Mouse	Fibroblasts	Col1a2	Fibroblasts	Tissue	Breast	32840210	eLife	Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in Mouse models of breast cancer	GSE123366
Mouse	Neural cells	"Cited4, Cd36, Aqp5"	Neu-3	Tissue	Breast	32840210	eLife	Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in Mouse models of breast cancer	GSE123366
Mouse	T cells	"CD3E, CD4, CD8A, Gzmb, Il7r"	T cells	NA	Breast	31611701	Nat Immunol	Multiplexed activation of endogenous genes by CRISPRa elicits potent anti-tumor immunity	GSE133983
Mouse	Epithelial cells	"Cdh1, Epcam"	Epithelial cells	NA	Breast	33024122	Nat Commun	Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence	PRJNA509416
Mouse	Mesenchymal cells	"Ddr2, Vim"	Mesenchymal cells	NA	Breast	33024122	Nat Commun	Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence	PRJNA509417
Mouse	T cells	"Cd3e, Cd8a, Cd28, Pdcd1"	T cells	Tissue	Breast	32117236	Front Immunol	Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.	NA
Mouse	Progenitor cells	"Krt5, Krt14, Krt15"	Oral epithelial progenitor cells	Tissue	Buccal mucosae	30472156	Cell Stem Cell	Perivascular Fibro-Adipogenic Progenitor Tracing during Post-Traumatic Osteoarthritis	GSE120654
Mouse	Glutamatergic cns	"Meis2, Lhx2"	Glutamatergic cns	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Meningeal cells	Foxc1	Meningeal cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Midbrain clusters	Tlx3	Midbrain clusters	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Purkinje cells	"Calb1, Car8"	Purkinje cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Roof plate	"Lmx1a, Msx1"	Roof plate	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Glial cells	"Hopx, Gdf10"	Bergmann glia cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Astrocytes	Slc1a3	Astrocytes	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Erythrocytes	"Hba-a2, Alas2, Hbb-bt, Fech"	Erythrocytes	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Neural cells	"Pax2, Lbx1"	Gabaergic interneurons	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Neural cells	"Atoh1, Pax6"	Glutamatergic neurons	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Microglia cells	"Tmem119, Itgam"	Microglia cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Oligodendrocytes	"Sox10, Olig1"	Oligodendrocytes	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Progenitor cells	"Id1, Msx3"	Early progenitor cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Endothelial cells	"Cd34, Pecam1"	Endothelial precursors	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Progenitor cells	"Lhx1, Lhx5"	Gabaergic progenitors	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Granular cells	Pax6	Granule neuron progenitors	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Progenitor cells	Hes5	Progenitor cells	Tissue	Cerebella	30220501	Current Biology	A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum	NA
Mouse	Cnv-ecs	"Top2a, Mki67"	PROLIFERATING CNV-ECS	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Cnv-ecs	"Pgf, Rhoc, Fscn1, Mcam, Trp53i11, Lama4"	TIP CNV-ECS	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Cnv-ecs	"Vwf, Mgp, Cfh, Cpe"	TRANSITIONING CNV-ECS	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Cnv-ecs	"Aplnr, Selp, Mmp2, Mmp14"	IMMATURE CNV-ECS	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Cnv-ecs	"Rgcc, Plpp1, Cd24a, Kdr"	NEOPHALANX CNV-ECS	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Peripheral cecs	"Gja4, Gkn3, Sox17, Hey1"	Arteries CECs	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Peripheral cecs	"Car4, Plvap"	Capillaries CECs	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Peripheral cecs	"Vwf, Selp"	Veins CECs	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Peripheral cecs	Prox1	Lymphatics CECs	Tissue	Choroid	32268117	Cell Metab	Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis	GSE77199
Mouse	Monocytes	Ly6C	Infiltrating monocytes	Tissue	Choroid	33038331	Dev Cell	Inflammation of the Embryonic Choroid Plexus Barrier following Maternal Immune Activation	NA
Mouse	Hec	Pmch	Hec	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Idc	"Otoa, Cdkn1c, Smoc2, Ptgds"	Idc	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Ipcs	"Emid1, Npy"	Ipcs	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Iphc	Matn4	Iphc	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Iscs	"Sox2, Cdkn1b, Prsss23"	Iscs	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Ko	"Calb1, Crabp1, Tectb"	Ko	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Oc90	"Oc90, Cndp2, Vmo1"	Oc90	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Opcs	"Fam159b, Ppp1r2, A100b, Serpine2, Smagp"	Opcs	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Satellite cells	Plp	Satellite cells	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85984
Mouse	Tympanic border cells	Emilin2	Tympanic border cells	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85986
Mouse	B cells	"Cx3cr1, Cd79a"	B cells	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85988
Mouse	Natural killer T (NKT) cells	Nkg7	Natural killer T (NKT) cells	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85989
Mouse	Glial cells	"Cnp, Cryab, Mbp, Mpz, Pmp22"	Glial cells	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Hair cells	"Myo6, Myo7a, Pvalb, Cib2, Ccer2, Acbd7, Rprm, Cd164l2"	Hair cells	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Hair cells	"Myo6, Myo7a, Pvalb, Cib2, Ccer2, Acbd7, Rprm, Cd164l2"	Hair cells	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Macrophages	"Cx3cr1, Cd79a"	Pan macrophages	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85987
Mouse	Dendritic cells	"Hes5, Igfbpl1, Lfng, Prss23, S100a1"	DC3	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Dendritic cells	"Apoe, Bmp4, Fbln2, Fst, Npnt"	CC/OSC	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Dendritic cells	"Lgr5, Fgf3, Lfng, Hes5, Pdzk1ip1, Ppp1r2, S100a1, Serpine2"	DC1/2	Tissue	Cochlea	32404924	Nat Commun	Characterization of the development of the Mouse cochlear epithelium at the single cell level	GSE137299
Mouse	Schwann cells	Plp	Schwann cells	Tissue	Cochlea	30063705	Plos Genetics5174	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85983
Mouse	Schwann cells	Mpz	Schwann cells	Tissue	Cochlea	30063705	Plos Genetics	High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a coreprogramming factor	GSE85985
Mouse	Immune cells	"Cx3cr1, Fcgr4, Ms4a7, Cd53, Lyz2"	Immune cells	Tissue	Cochlea	32938973	Sci Rep	The immune response after noise damage in the cochlea is characterized by a heterogeneous mix of adaptive and innate immune cells	NA
Mouse	Early endosomes	EEA1	Early endosomes	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	Muscle cells	"Myh11, Des"	Enteric smooth muscle	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Intestinal stem cells	"Lgr5, Olfm4, Ascl2"	Intestinal stem cells	Tissue	Colon	33060802	Mucosal Immunol	"IL-22 receptor signaling in Paneth cells is critical for their maturation, microbiota colonization, Th17-related immune responses, and anti-Salmonella immunity"	GSE159423
Mouse	Late-endosoma	"LAMP1, LAMP2, Rab7A"	Late-endosoma	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	Mesenchymal cells	"Acta2, Vim, Myh11"	Putative myofibroblast	Tissue	Colon	29875413	Nature	GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells	GSE113043
Mouse	Mesenchymal cells	"Acta2, Vim, Foxl1"	Subepithelial mesenchymal cells	Tissue	Colon	29875413	Nature	GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells	GSE113044
Mouse	Macrophages	"GBP2, GBP2b, GBP3, GBP4, GBP5, GBP6, GBP7, GBP8, GBP9"	Activated human macrophages	Tissue	Colon	31375632	Proc Natl Acad Sci U S A	Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the antitumor response under PD-1 blockade.	NA
Mouse	Epithelial cells	"Epcam, Krt19"	Epithelial cells	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Endothelial cells	Lyve1	Lymphatic endothelial cells (LECs)	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Endothelial cells	Pecam1	Vascular endothelial cells	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Fibroblasts-like cells	"Dpt, Col6a2, Col1a2"	Fibroblasts-like cells	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Glial cells	"S100b, Gfap"	Glial cells	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Glial cells	S100b	Glial cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Hematopoietic cells	"Cd52, Cd45"	Hematopoietic cells	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ Integrin beta7+	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34- CD16/32-	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32- CD115lo	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32- Flt3+ CD115hi	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32hi Ly6C-CD115lo	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32hi Ly6C+CD115lo	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32hi Ly6C+-CD115hi	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- c-Kit+ CD34+ CD16/32hi FcER+	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Hematopoietic cells	NA	Lin- Sca1- CD34+ c-Kit- CD125+	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	Interstitial cells	"Kit, Ano1"	Interstitial cells of Cajal	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Myeloid cells	CD11b	Myeloid cells	Tissue	Colon	31375632	Proc Natl Acad Sci U S A	Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the antitumor response under PD-1 blockade.	NA
Mouse	Macrophages	"Arg1, CD45, Gpb2b, Bst1"	Arg1A macrophage	Tissue	Colon	30613266	Theranostics	Arg1 expression defines immunosuppressive subsets of tumor-associated macrophages.	GSE112865
Mouse	Macrophages	"Arg1, CD45, Sgk1, Pmepa1, Ms4a7"	Arg1B macrophage	Tissue	Colon	30613266	Theranostics	Arg1 expression defines immunosuppressive subsets of tumor-associated macrophages.	GSE112865
Mouse	Macrophages	"CD11b, MHCII, F4, F80, CD103"	Interstitial macrophages	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	Macrophages	"H2-Eb1, H2-Ab1, H2-Aa , H2-DMa , H2-DMb1, CXCL9, CXCL10, CCL5, CCL8, IL2rg, Stat1, Fcgr4, Fam26f"	Macrophages with an M1-type signature	Tissue	Colon	31375632	Proc Natl Acad Sci U S A	Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the antitumor response under PD-1 blockade.	NA
Mouse	Macrophages	"CD45, CD11b, F4, F80, CD64, MHCII"	Macrophages	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	Pericytes	"Rgs5, Pdgfrb"	Pericytes	Tissue	Colon	30270042	Cell	Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease	"GSE95459, GSE114374"
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Colon	32367039	Cell Research	Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer	GSE142694
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Colon	32367039	Cell Research	Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer	GSE142694
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Colon	32367039	Cell Research	Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer	GSE142694
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Colon	32367039	Cell Research	Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer	GSE142694
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Colon	32367039	Cell Research	Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer	GSE142694
Mouse	Pericytes	Rgs5	Pericytes	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Mast cells	"Car1, Car2"	Mast cells progenitors	Tissue	Colon	32421753	PLoS Pathog	Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell	GSE131059
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Colon	33238123	Cell Rep	An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets	GSE159208
Mouse	Epithelial cells	"Car1, Muc2, Car4, Krt19, Krt8, Krt18"	Epithelial cells	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	Fibroblasts	"Acta2, Dcn, Des, Lamb1, Lama4, Lamc1, Tpm2, Nid1"	Fibroblasts	Tissue	Colon	32970988	Cell	Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption	GSE146131
Mouse	CD4 T cells	CD4	CD4 T cells	Tissue	Colon	33022229	Immunity	"T Cell Receptor Is Required for Differentiation, but Not Maintenance, of Intestinal CD4 Intraepithelial Lymphocytes."	GSE157453
Mouse	T cells	Sell	Naive T cell	Tissue	Colon	33238123	Cell Rep	An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets	GSE159208
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Epcam, Krt19, Lgr5, Axin2, Mki67"	Intestinal epithelial stem cells and transit-amplifying cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Epcam, Krt19, Atoh1, Muc2"	Goblet cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Epcam, Krt19, Atoh1, Reg4"	Deep crypt secretory cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Epcam, Krt19, Guca2a, Alpi, Aldh1l1"	Enterocytes	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Epcam, Krt19, Chga, Chgb, Neurod1"	Enteroendocrine cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Stromal cells	"Vim, Col1a1"	Stromal cells	Tissue	Colon	33306673	Plos Biol	Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis	GSE151257
Mouse	Epithelial cells	"Krt13, Krt19, Muc4"	Conjunctival epithelial cells	Tissue	Cornea	31419300	Invest Ophthalmol Vis Sci	Single-Cell RNA Transcriptome Helps Define the Limbal/Corneal Epithelial Stem/Early Transit Amplifying Cells and How Autophagy Affects This Population	NA
Mouse	Epithelial cells	"Cdh1, Pax6, Krt15"	Epithelial cells	Tissue	Cornea	31419300	Invest Ophthalmol Vis Sci	Single-Cell RNA Transcriptome Helps Define the Limbal/Corneal Epithelial Stem/Early Transit Amplifying Cells and How Autophagy Affects This Population	NA
Mouse	Mesenchymal cells	"Vim, Lum, Kera"	Mesenchymal cells	Tissue	Cornea	31419300	Invest Ophthalmol Vis Sci	Single-Cell RNA Transcriptome Helps Define the Limbal/Corneal Epithelial Stem/Early Transit Amplifying Cells and How Autophagy Affects This Population	NA
Mouse	Committed opc	"Ptprz1, Serpine2, Ptgds, Car2, Il33"	Committed opc	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	NA	Myelin forming oligodendrocyte 1	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Ptgds, Car2"	Myelin forming oligodendrocyte 2	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Ptprz1, Serpine2, Ptgds, Car2"	Newly formed oligodendrocyte1	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Erg1, Dusp1, Fosb, Anxa5, Ptgds, Grm3, Car2, Il33"	Mature oligodendrocytes 1	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Klk6, Hopx, Anxa5, Car2"	Mature oligodendrocytes 2	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Klk6, Hopx, Anxa5, Ptgds, Car2"	Mature oligodendrocytes 3	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Erg1, Dusp1, Fosb, Klk6, Hopx, Anxa5, Ptgds, Grm3, Car2"	Mature oligodendrocytes 4	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Ptgds, Car2, Il33"	Mature oligodendrocytes 5	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Ptgds, Car2, Il33"	Mature oligodendrocytes 6	NA	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Oligodendrocytes	"Ptprz1, Serpine2, Erg1, Dusp1, Fosb, Ptgds, Car2"	Oligodendrocyte progenitors	Tissue	Corpus callosum	33203872	Nat Commun	Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury	GSE128525
Mouse	Astrocytes	Gja1	Astrocytes	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	NA
Mouse	Endothelial cells	Flt1	Endothelial cells	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	NA
Mouse	Neural cells	Slc17a7	Excitatory neurons	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	GSE106678
Mouse	Neural cells	Gad2	Inhibitory neurons	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	NA
Mouse	Microglia cells	Ctss	Microglia cells	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	GSE106678
Mouse	Oligodendrocytes	"Mog, Enpp6"	Oligodendrocytes	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	GSE106678
Mouse	Oligodendrocytes	Pdgfra	Oligodendroglial precursors	NA	Cortices	29220646	Molecular Cell	Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq	NA
Mouse	Mesenchymal cells	"Dcn, Lum, Gsn"	Mesenchymal cells	Tissue	Descending aorta	31141696	Cell Rep	Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells	NA
Mouse	Endothelial cells	"Sox17, Cd36, Fabp4, Cldn5"	Vascular endothelial cells	Tissue	Descending aorta	31141696	Cell Rep	Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells	NA
Mouse	Satellite cells	"Pax7, Pax3, Myod1, Myf5"	Satellite cells	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	Cd3d	T cells	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	Cd19	B cells	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Progenitor cells	Pdgfra	Fibro-adipogenic progenitors	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	"Itgam, Fcer1g, C1qa"	Macrophages	Tissue	Diaphragm	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Bone	"Bglap, Ibsp, Spp1"	Bone	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Pericytes	"Myh11, Rgs5, Mylk, Pdgfrb"	Pericyte cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Macrophages	"Adgre1, C1qa, Lyz2"	Macrophages	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Endothelial cells	"Pecam1, Tie1, Cdh5"	Endothelial cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Epithelial cells	"Krt5, Krt14, Krt10"	Epithelial cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Immune cells	"Aif1, Tnfrsf11a, Tnfrsf13b"	Immune cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Mesenchymal cells	"Pdgfra, Pdgfrb, Prrx2"	Mesenchymal cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Endothelial cells	"Pecam1, Cd93, Egfl7"	Endothelial cells	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Epithelial cells	"Krt14, Krt42, Perp"	Epithelial cells	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Fibroblasts	"Prrx1, Msx1, Vim"	Fibroblasts	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Monocytes	"Lyz2, Cd14, Cd86"	Monocytes	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Muscle cells	"Rgs5, Notch3, Myh11"	Vascular smooth muscle cells	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Schwann cells	"Sox10, Sox2, Plp1"	Schwann cells	Tissue	Digit tip	31902657	Dev Cell	Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration	GSE135985
Mouse	Schwann cells	"Plp1, Mbp, Scn7a"	Schwann cells	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	T cells	"Cd3g, Icos, Trdc"	T cells	Tissue	Digit tip	32097654	Dev Cell	Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution	GSE143888
Mouse	Stem cells	"Olfm4, Gkn3, Igfbp4"	Stem-like cells	Tissue	Duodenum	32350281	Nat Commun	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier	PRJNA573959
Mouse	Enterocytes	"Creb3l3, Ace2, Slc2a2"	Enterocytes	Tissue	Duodenum	32350281	Nat Commun	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier	PRJNA573959
Mouse	Enteroendocrine cells	"Chga, Tph1, Gcg, Ghrl, Reg4, Amigo2, Etv1, Gip, Pkib, Sst, Iapp, Sphkap, Asic5, Hhex"	Enteroendocrine cells	Tissue	Duodenum	32350281	Nat Commun	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier	PRJNA573959
Mouse	Goblet cells	"Clca1, Muc2, Tff3, Ano7"	Goblet cells	Tissue	Duodenum	32350281	Nat Commun	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier	PRJNA573959
Mouse	Tuft cells	"Alox5ap, Lrmp, Dclk1"	Tuft cells	Tissue	Duodenum	32350281	Nat Commun	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier	PRJNA573959
Mouse	Epidermis	"Krt17, Krt14"	Epidermis	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Sesc	"Coch, Otol1"	Sesc	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Glial cells	"Top2a, Plp1, 2810417H13Rik, Cfd, Gfap"	Glial cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Hair cells	"TMC1, Myo7a, Pvalb, Otof, Ush1C, Espn, Cabp2, Kcna10"	Hair cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Adipocytes	"Adipoq, Pgf, Ptx3"	Adipocytes	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Epithelial cells	"Cldn3, Hoxa10, Mt4, Cldn10, Epcam, Cldn9"	Epithelial cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Mesenchymal cells	"Clcx1, Twist2, Spp1, Sfrp2, Car9"	Mesenchymal cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Muscle cells	"Tnnc1, Myf5, Gm7325, Myog"	Muscle cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Neural cells	"Tubb3, Nm1, Rtn1, Ngfr"	Neurons	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Neural cells	"Slc6a13, Slc7a11, Gfap"	Neurons_glia cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Oligodendrocytes	Olig1	Oligodendrocytes	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Stem cells	Pou5f1	Stem cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Stromal cells	"Clec3b, Pgf, Snhg6, Mfap5, Vtn, Cilp, Mmp11"	Stromal cells	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Keratinocytes	Cxcl13	Keratinocytes	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Neural cells	Hes5	Neural precursors	Organoids	Ear	31204303	Stem Cell Reports	Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids	GSE130649
Mouse	Epithelial cells	"Krt18, Krt19, Epcam, Krt5, Krt14"	Basal epithelial cells	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Epithelial cells	"Krt18, Krt19, Epcam, Spag6l, Hydin"	Ciliated epithelial cells	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Epithelial cells	"Krt18, Krt19, Epcam, Muc1, Lyz"	Secretory epithelial cells	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	T cells	"Ptprcap, Cd3d"	T-cell	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	B cells	"Ptprcap, Cd79a"	B-cell	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Lymphocyte cells	"Ptprcap, Areg"	Type 2 lymphoid cells	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Macrophages	Adgre1	Macrophages	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Monocytes	"Adgre1, C1qa"	M2 Macrophages	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Dendritic cells	Itgax	Dendritic cells	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Monocytes	Klrk1	Cytotoxic phenotype monocytes	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Stromal cells	"Col1a2, Egfl7, Flt4"	Vascular Endothelial cellss	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Stromal cells	"Col1a3, Egfl7, Flt1"	Lymphatic Endothelial cellss	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Stromal cells	"Col1a4, Rgs5"	Pericytes	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Stromal cells	"Col1a5, Mlana"	Melanocytes	Tissue	Ear	32351546	Front Genet	Single-Cell Transcriptomes Reveal a Complex Cellular Landscapein the Middle Ear and Differential Capacities for Acute Responseto Infection	GSE146244
Mouse	Na_ve pluripotent cells	"1110008L16Rik, 1810037I17Rik, 2810008D09Rik, Akap12, Akr1b3, Alg13, Alpl, Apoc1, Apoe, Arid5b, Ash2l, Asns, Atox1, Atp5g1, AU018091, Avpi1, Bax, Baz2a, BC033916, Bcat1, Bex1, Bpnt1, Calcoco2, Cbr3, Cbx7, Cd9, Cebpzos, Chchd10, Cisd1, Ckb, Cldn4, Col18a1, Cox4i1, Csrp2, Ctbp2, Dbi, Dhx16, Dna"	Na_ve pluripotent cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Germ cells	"1500012F01Rik, 2410006H16Rik, 2610524H06Rik, Acadl, Acer2, Acot1, Acot13, Akr7a5, Aldh2, Aldh5a1, Alox15, Apoe, Aspscr1, Avpi1, Bbx, Bckdha, Bst2, Btf3l4, Capg, Ccno, Ccpg1os, Cdc42ep5, Cdk2ap2, Cdkn1c, Cdx2, Cenpw, Cir1, Cldn7, Cmas, Cnot11, Col18a1, Coro1b, Cox7a2, Cpm, Crip1, Crot, Ctps2"	Primordial germ cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Cardiac cells	"Abracl, Acta1, Acta2, Actb, Actc1, Actg1, Anxa3, Arl4c, Arpc5, Bambi, Bex1, Bmp4, Cabp1, Car2, Cd9, Cdc42ep5, Cdkn1a, Cdkn1c, Cited2, Clic1, Cnih4, Cnn1, Cnn2, Cnn3, Crip2, Csrp1, Cst3, Cyb5a, Cyr61, Dstn, Eno3, Gata3, Glipr2, Gng2, Gpx7, Hes1, Hspb1, Id1, Id3, Ier5, Ifitm3, Isl1, Krt18, Krt19, Krt"	Cardiac cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Endoderm cells	"2410006H16Rik, Aes, Aldoa, Amot, Anxa2, Anxa4, Apoe, Blvrb, Bnip3, Bnip3l, Bsg, Car4, Cd24a, Cdh1, Cer1, Cers4, Cfc1, Chchd10, Cited1, Cldn6, Cldn7, Clic6, Col9a3, Commd7, Cotl1, Crb3, Crip1, Ctsz, Cyba, Cystm1, Dapk2, Ddah2, Ddit4, Dgkk, Dkk1, Dnmt3b, Dpysl3, Dusp4, Eef2, Ehd1, Elf3, Emb, Epcam"	Endoderm cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Hematopoietic cells	"AA465934, Ablim1, Amot, Aplnr, Apoe, Aprt, Arpc1b, Atp2b1, Bambi, Calm2, Car4, Cbfa2t3, Ccnd1, Cd59a, Cd9, Cited2, Clic1, Col18a1, Col4a2, Creg1, Crip2, Ctsh, Ddah2, Dusp2, Ebf1, Ecscr, Egfl7, Ets1, Etv2, Exoc3l, F2r, Fam212a, Fgf3, Fli1, Fn1, Fth1, Gadd45g, Gata2, Gchfr, Gngt2, Herc1, Hhex, Id3"	Hematopoietic cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Muscle cells	"9-Sep, 6330403K07Rik, 6330419J24Rik, Abracl, Acta2, Actb, Actc1, Actg1, Ahnak, Akap12, Amot, Anxa2, Appbp2, Aprt, Arhgdia, Arl2bp, Arl4c, Arpc5, Asb4, Atg3, Bambi, Basp1, BC023829, Bmp4, C430049B03Rik, C530008M17Rik, Cald1, Calm2, Cap1, Capn2, Capn6, Car4, Ccnd1, Ccnd2, Cd24a, Cdc42ep5, Cdk"	Smooth muscle cells	Tissue	Embryoid body	31740535	Development	Single cell transcriptome dynamics from pluripotency to FLK1+_esoderm	GSE130146
Mouse	Cxcl12 co-expressed	"Il1r1, Col3a1, Col5a2, Igfbp5, Sned1, Ifi203, Nenf, Pfkfb3, 1110008P14Rik, Lcn2, Serping1, Ube2l6, Fibin, B2m, Eid1, Fgf7, Cpxm1, Ism1, Cst3, Lbp, Wisp2, Zbp1, Srpx, Il13ra1, Apln, Hs6st2, Bgn, Slc16a2, Capn6, Gpm6b, Cp, Dclk1, Mme, Ptx3, Tbx15, Slc16a1"	Cxcl12 co-expressed	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Ecm.rearrangement	"Sulf1, Col19a1, Col3a1, Col5a2, Fn1, Ihh, Col4a4, Col4a3, Serpinb5, Fmod, Elf3, Lamc1, Tnr, Dpt, Ddr2, Olfml2b, Tgfb2, Itga8, Adamtsl2, Col5a1, Pomt1, Eng, Lmx1b, Gsn, Olfml2a, Creb3l1, Hsd17b12, Wt1, Grem1, Spint1, Cst3, Fkbp1a, Mmp9, Sulf2, Atp7a, Nox1"	Ecm.rearrangement	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Embryonic mesenchyme	"Matn4, Matn1, Col9a1, Col9a3, Cnmd, Asb4, Col9a2, Wwp2, Sox9, Col2a1, Nnat, Hapln1, Cytl1, Cd24a, Mest, Mia, Bex2, Mpz, Cdkn1c, Papss2, Stmn1, Ldha, Plod2, Cdk4, Slc26a2, Bex3, Epyc, Pdia6, Ss18l2, S100b, Crabp1, Fibin, Siva1, Gpc3, Cthrc1, Tpi1, Hnrnpd"	Embryonic mesenchyme	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Er.stress	"Nck2, Ankzf1, Dnajb2, Rhbdd1, Bcl2, Ubxn4, Yod1, Ppp1r15b, Fam129a, Edem3, Atf6, Ufc1, Atf3, Man1b1, Tor1a, Hspa5, Dab2ip, Nfe2l2, Dnajc10, Psmc3, Creb3l1, Thbs1, Eif2ak4, Chac1, Pdia3, Bcl2l11, Ddrgk1, Tmx4, Trib3, H13, Edem2, Cebpb, Ptpn1, Vapb, Srpx, A"	Er.stress	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Ifitm1 co-expressed	"1500015O10Rik, Crocc2, Sned1, Fmod, Serping1, Cst3, Ptgis, Slc16a2, Fabp5, Cp, Gper1, Gng11, Cemip, Adm, Ifitm2, Ifitm1, H19, Akap12, Gja1, 1500009L16Rik, Scara5, Zic5, Mmp13, Clmp, Ctsh, Zic1, Zic4, Ebf1, Sfrp4, Tgfbi, Hif1a, Aspg, Fbln1, Kng2, Apod, Abi"	Ifitm1 co-expressed	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Long-term mefs	"Rps3a3, Timp1, Bex1, Rhox5, Gm15459, S100a6, Gm10320, Gsto1, Gm11942, S100a4, Gm10260, Mif, Esd, Gm15772, Anxa1, Ctgf, Rps27l, Pkm, Bex3, Txn1, Tagln2, Tnfrsf12a, Ldha, Selenoh, Serpinb2, Gm28438, Tex19.1, Gm10263, Tubb5, Birc5, Ran, Anxa2, Gsta4, Nme1, T"	Long-term mefs	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Matn4 co-expressed	"Spats2l, Igfbp5, Kcns1, Matn4, Penk, Mfap2, Eln, Cpxm2, Pdgfrl, Igfbp3, Mfap4, Igfbp4, Nov"	Matn4 co-expressed	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Mef.identity	"Gm5571, Rbfox2, Btbd19, Actn1, Gatad2a, Med6, Mex3a, Ccdc80, Mex3c, Sdpr, Pcdhb2, Trim16, Obsl1, Epha1, Stx1b, Stau1, Serpine1, Aa881470, Col12a1, 2010300f17rik, Ccdc102a, Nradd, Pard6g, Ntn4, 5730471h19rik, Sepn1, Peg12, Dpysl3, 1110012d08rik, Akt1, Zfp2"	Mef.identity	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Pluripotency cells	"Gm5Rhox5, Tdgf1, Utf1, Mkrn1, Dppa5a, Upp1, Chchd10, Klf2, Trap1a, Mylpf, 1700013H16Rik, AA467197, Dhx16, Mt2, Ube2a, Khdc3, Pycard, Hsp90aa1, Prrc1, Hat1, Calcoco2, Impa2, Saa3, Ooep, Bnip3, Mt1, Asns, Aldoa, Tdh, Gjb3, Rbpms2, Prps1, Fam25c, Eif2s2, Cen"	Pluripotency cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Proliferating cells	"Mcm4, Smc4, Gtse1, Ttk, Rangap1, Ccnb2, Cenpa, Cenpe, Cdca8, Ckap2, Rad51, Pcna, Ube2c, Lbr, Cenpf, Birc5, Dtl, Dscc1, Cbx5, Usp1, Hmmr, Wdr76, Ung, Hn1, Cks2, Kif20b, Cdk1, Slbp, Aurkb, Kif11, Cks1b, Blm, Msh2, Gas2l3, Tyms, Hjurp, Hells, Prim1, Uhrf1, N"	Proliferation	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Senescence	"Il6, Il7, Il1a, Il1b, Il13, Il15, Cxcl15, Cxcl1, Cxcl2, Cxcl3, Ccl8, Ccl13, Ccl3, Ccl20, Ccl16, Ccl26, Csf2, Mif, Areg, Ereg, Nrg1, Egf, Fgf2, Hgf, Fgf7, Vegfa, Ang, Kitl, Cxcl12, Pigf, Igfbp2, Igfbp3, Igfbp4, Igfbp6, Igfbp7, Mmp1, Mmp3, Mmp10, Mmp12, Mmp"	Senescence	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Giant cells	"Car2, Sct, 1500009L16Rik, Serpinb9e, Prl2a1, S100a6, Plac8, Serpinb9g, Prl6a1, Lgals9, Prl7b1, Ada, Aldh1a3, Serpinb6b, Sri, Fstl3, Serpinb9d, Prl2c5, H19, Aprt, Serpinb9c, Ascl2, Plac1, Mt2, Fthl17a, Trp53i11, Mrfap1, Phactr1, Tnfrsf9, Lgals1, Pitrm1, Nc"	Spiral artery trophpblast giant cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Spongiotrophoblasts	"Phlda2, Dio3, Dkkl1, Hspb1, Tmem14c, Cidea, Tfrc, Batf3, Sin3b, Prss8, Ldoc1, Maoa, Cdkn1c, Las1l, Rhox6, Tex19.1, 2610528J11Rik, Gkap1, Cldn7, Slc22a18, Rhox9, Mrps6, Serpinb9g, Aqp3, mt-Cytb, Hsp25-ps1, Rdh12, Krt18, Pfdn1, Tulp1, Selenoh, Dynll2, Glrx5"	Spongiotrophoblasts	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Trophoblast.identity	"Sct, Rhox9, Rhox6, Ldoc1, Sin3b, Fthl17a, Cdkn1c, Gm9112, Rhox5, 3830417A13Rik, Plac1, Serpinb9g, Serpinb9e, Tbrg1, Mbnl3, Trap1a, Hspb1, Dusp9, Nup62cl, Phlda2, Krt8, Tex19.1, H19, Serpinb9b, Lgals1, Krt19, Rps4l, Hmgn5, Gm9, Gjb5, Epop, Lgals9, Gjb3, Sl"	Trophoblast.identity	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Two c (2c)	"BB287469, Zscan4f, Gm5662, Gm9125, Gm2016, Obox3, Gm11544, Gm428, Gm4850, Dub1a, Cdkn2d, Usp17l5, Gm2022, Gm1995, Gm4303|Gm4305|Gm4307, H47, Omt2b, Zscan5b, Gm11756, Gm13078, Gm10696, Omt2a, Gm8300, Gm4971, Gm11487, 1600025M17Rik, Gm5039, Ube2d2, Zfp707"	Two c (2c)	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Xen	"Dab2, Fst, Pdgfra, Pth1r, Gata6, Foxq1, Fxyd3, Tet3, Sox17, Foxa2, Lama1, Lamb1, Gata4, Krt8"	Xen	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Apoptotic cells	"Ercc5, Serpinb5, Inhbb, Steap3, Btg2, Phlda3, Tnni1, Rgs16, Ier5, Slc19a2, Adck3, Ephx1, Ptpn14, Atf3, Notch1, Rxra, Ralgds, Ak1, Stom, Ddb2, Cd82, Il1a, Pcna, Bmp2, Trib3, Procr, Blcap, Ada, Fgf13, Irak1, Tspyl2, Sat1, Zmat3, Hspa4l, Slc7a11, Tm4sf1, Rap"	Apoptotic cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Astrocytes	"Gja1, Gjb6, Cldn10, F3, Slc1a3, Slc39a12, Sdc4, Acsbg1, Mfge8, Ntsr2, Lcat, Cml5, Aqp4, Pla2g7, Ppap2b, Ppp1r3c, S1pr1, Slc25a18, Plcd4, Chrdl1, Fam107a, Dio2, Gpr37l1, Mt2, Entpd2, Gstm1, Cbs, Tst, Prodh, Slco1c1, Gfap, Tlcd1, Mlc1, Apoe, C030018K13Rik"	Astrocytes	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Neural cells	"Nos1, Fam84a, Unc5d, Rnd2, Pou3f2, Pdzrn3, Hs3st1, Sstr2, Pcp4, Meis2, Lrrc16b, Plekhf2, Sorl1, Ppp2r2b, Trim9, Pou3f1, Frmd4b, Mllt3, Plcb1, Ppp2r1b, Lsamp, Enc1, Robo2, Scrt2, Cdh4, Slc17a6, Osbpl6, Sema3c, Kif21b, Wnt7b, Tbr1, Chga, Tenm4, Lmo1, Tsc22d"	Cortical neurons	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Neural cells	"Vtn, Ednrb, Sox21, Zeb2, Hes5, Fabp7, Sox1, Neurod1, Pax3, Pax6, Cdh2, Sox9, Sox2, Id2, Hoxb1, Msx1, Msi1, Msi2, Atoh1, Rbfox3, Map2, Tubb3"	Aeural cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Oligodendrocytes	"Spp1, Ccnb1, Pdgfra, Dcn, Rlbp1, Slc6a13, Inmt, Pnlip, Lum, Cmbl, Pcolce, Postn, Apod, Ednrb, Scrg1, Tmem45a, Fam70b, Cspg4, Cacng4, Fabp7, Pbk, 1110015O18Rik, Emid1, Serping1, Olig1, Vtn, Prc1, Fam180a, E130306D19Rik, Bgn, Lmcd1, Col1a2, Spc25, Calcrl, I"	Oligodendrocyte precursors	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Epithelial cells	"Cdh1, Tgm1, Cldn3, Cldn4, Cldn7, Cldn11, Ocln, Epcam, Crb3, Krt8, Krt19, Pkp3, Dsp, Pkp1"	Epithelial.identity	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Glia cells	"Gdf10, Id3, Tesc, Thrsp, Tnfrsf19, Frzb, Id1, Sdpr, Emid1, E330013P04Rik, Hspb8, Pdlim3, Dcn, Gfap, X1500015O10Rik, Mt2, Lef1, Rmst, Gas1, Tst, Mgll, Zic5, Sp5, Hopx, Prex2, Eya1, X0610040J01Rik, Cav1, Mt1, Adamts19, Wnt8b, Nme7, Crip1, Zfp36l1, Cyp1b1, L"	Radial glia cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Glia cells	"Id3, Id1, Foxj1, Mt1, Mt2, Pla2g7, Hes5, Hes1, Mia, Egr1, Metrn, Fos, Tmem47, Ednrb, Tppp3, Clu, Serpine2, Riiad1, Gfap, Sparcl1, Apoe, Slc1a3, Nlrx1, Selm, Ttyh1, Gstm1, Lxn, Cyr61, Fbxo2, Mlc1, Enkur, Mlf1, Mgst1, Slc9a3r1, Bcan, Fabp7, Dbi, Emp2, Ppp1r"	Radial glia cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Glia cells	"Neurog2, Eomes, Gadd45g, Rhbdl3, Ptgds, Btbd17, Snhg18, Lima1, Tfap2c, Mfng, Btg2, Myo10, Csrp1, Tead2, Pax6, Celsr1, Gm29260, Chd7, Acads, Heg1, Dll1, Gamt, Kcne1l, Tox3, Rcn1, Gfap, Igfbp5, Hes6, Efhd2, Inppl1, Lrrn3, Sfrp1, Nme4, Sox21, Loxl1, Fam210b"	Radial glia cells	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Progenitor cells	"Rhox6, Rhox9, 3830417A13Rik, Gjb3, Gm9112, Hspb1, Nup62cl, Ldoc1, Hspe1, Rhox12, Tex19.1, Gjb5, Sin3b, 1700086L19Rik, Ldhb, Krt19, Hmgn5, Trap1a, Plac1, Cdkn1c, Bex1, Fthl17a, Dbi, Ube2a, Dnaja1, Phactr1, Phlda2, Hand1, Selenoh, Rhox5, Atp5g1, Hmgn1, Hat1"	Trophoblast progenitors	Cell line	Embryonic fibroblasts	30712874	Cell	Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming	GSE122662
Mouse	Embryonic/fetal myoblasts	"Acta2, Tagln"	Embryonic/fetal myoblasts	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131734
Mouse	Epiblast	Fgf5	Epiblast	Cell line	Embryonic stem cells	32795399	Cell Stem Cell	Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation	GSE114952
Mouse	Mesoderm	"mesoderm factors T , Eomes"	Mesoderm	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131738
Mouse	Pluripotency cells	"Zfp42, Nanog, Pou5f1"	Pluripotency cells	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131737
Mouse	Ectoderm cells	"Sox2, Pax3"	Ectoderm cells	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131740
Mouse	Mesenchymal cells	"Col1a1, Col1a2, Col3a1, Acta2, Tagln"	Mesenchymal cells	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131735
Mouse	Mesenchymal cells	"Col1a1, Col1a2, Col3a1"	Mesenchymal cells	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131736
Mouse	Endoderm cells	"mesoderm factors T , Eomes, Foxa2, Gsc"	Mesendodermal	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131739
Mouse	Neural cells	Vimentin	Neural progenitors	Cell line	Embryonic stem cells	29313530	Cell Res	Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers	GSE74055
Mouse	Ectoderm cells	SOX1	Neuroectoderm cells	Cell line	Embryonic stem cells	32795399	Cell Stem Cell	Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation	GSE114952
Mouse	Progenitor cells	"Myod1, Myog, Tnni1"	Skeletal myogenic progenitors	Cell line	Embryonic stem cells	31590918	Biochem Biophys Res Commun	Single-cell RNA-seq analysis of Mesp1-induced skeletal myogenic development.	GSE131734
Mouse	Caudal epiblast	Nkx1-2	Caudal epiblast	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Caudal mesoderm	"Cdx2, Cdx1"	Caudal mesoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Ecto	"Sox2, Otx2, Pax6, Ptn, Hes3"	Ecto	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Eecto	"Tfap2c, Gata2, Elf5"	Eecto	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Eendo	"Afp, Spink1, Apoa4, Hnf4a"	Eendo	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Emeso	"Foxf1, Bmp4, Plagl1"	Emeso	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Epiblast	"Dnmt3b, Utf1"	Epiblast	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Gut	Apela	Gut	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Ice_epi	"Gapth, Ppia, pou5f1"	Ice_epi	Cell line	Embryos	31626770	Cell	Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures	GSE135701
Mouse	Intermediate	"Gapth, Ppia, Pou5f1, T"	Intermediate	Cell line	Embryos	31626770	Cell	Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures	GSE135701
Mouse	Lymph	"Lyve1, Prox1"	Lymph	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Lymph	"Lyve1, Prox1"	Lymph	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchyme	"Bmp4, Ahnak, Pmp22"	Mesenchyme	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Meso	"Hoxb1, T, Cdx1, Meox1, Hand1, Twist1, Twist2"	Meso	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Mixed mesoderm	Osr1	Mixed mesoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Nascent mesoderm	"Mesp1, Lefty2, Mesp2"	Nascent mesoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Nmp	"Hes3, Epha5, Cdx4, Hoxb9"	Nmp	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Notochord cells	"Foxa2, Chrd, Noto"	Notochord cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Paraxial mesoderm	"Tbx1, Meox1, Tcf15"	Paraxial mesoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Pe	"Gapth, Ppia, Dab2, Krt8, Krt18"	Pe	Cell line	Embryos	31626770	Cell	Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures	GSE135701
Mouse	Pgc	"Ifitm3, Dnd1, Dppa3"	Pgc	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Pluripotency cells	"Sox2, Nodal, Nanog"	Pluripotent epiblast (epi)	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Primitive streak	"Nanog, Eomes"	Primitive streak	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Germ cells	"Dppa3, Pou5f1, Klf5"	Primordial germ cells	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Germ cells	Dppa3	Primordial germ cells	Tissue	Embryos	32728215	Nature	Epigenetic regulator function through Mouse gastrulation	GSE137337
Mouse	Somitic mesoderm	"Aldh1a2, Dll1, Tbx6"	Somitic mesoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Te	"Gapth, Ppia"	Te	Cell line	Embryos	31626770	Cell	Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures	GSE135701
Mouse	Anterior primitive streak cells	"Otx2, Miixl1, Gsc, Lhx1, Pax7"	Anterior primitive streak cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Anterior visceral endoderm	"Cer1, Dkk1, Hhex, Lefty1"	Anterior visceral endoderm	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Blood cells	"Gata1, Klf1"	Blood cells	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Cardiomyocytes	"Smarcd3, Acta2, Tagin, Myl7, Nkx2-5, Myl4, Tnnt2"	Cardiomyocytes	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endoderm cells	Cer1	Definitive endoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Allantois	"Hoxa11, Hoxa2, Tbx4"	Allantois	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endothelial cells	"Anxa5, Pccam1, Cdh5"	Endothelial cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Ebf1, Mgp, Lhfp"	OE.1	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Rprm, Pcdh19, Ctxn3"	OE.2	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Fgf17, Mecom, Clu"	Anterior medial NaP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Barx1, Gm12446, Dmrt2"	Palate	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Shh, Fgf8, Lmo2"	Dental	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Col9a1, Adamts9, ltga4"	Fusion zone	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Gjb6, Barx2, Gap43"	NL groove	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Wnt9b, Wnt3, Lmo1"	Surface.1	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Robo2, Wnt3, Pcp4, Pcp1"	Surface.2	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Gabrp, Rhov, Lypd3"	Periderm	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Runx1t1, Tnfaip2, Snai1"	Ect & mes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Ebf1, Mgp, Lhfp"	OE.1	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Rprm, Pcdh19, Ctxn3"	OE.2	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Fgf17, Mecom, Clu"	Anterior medial NaP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Barx1, Gm12446, Dmrt2"	Palate	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Shh, Fgf8, Lmo2"	Dental	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Col9a1, Adamts9, ltga4"	Fusion zone	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Gjb6, Barx2, Gap43"	NL groove	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Wnt9b, Wnt3, Lmo1"	Surface.1	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Robo2, Wnt3, Pcp4, Pcp1"	Surface.2	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Gabrp, Rhov, Lypd3"	Periderm	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	"Epcam, Igfbp5, Pdgfa, Sfn, Spint2, Cre, LacZ, Runx1t1, Tnfaip2, Snai1"	Ect & mes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Ectoderm cells	Krt14	Ectoderm cells	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Endoderm cells	"Lhx1, Lefty1"	Embryonic visceral endoderm	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Ectoderm cells	"Elf5, Ascl2, Tfap2c"	Exe ectoderm cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endoderm cells	"Tfap2c, Ttr"	Endoderm cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endoderm cells	"Apln, Msx1"	Extra-embryonic visceral endoderm (exve)	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endothelial cells	"Foxa2, Sox17"	Endothelial cells	Tissue	Embryos	31086336	Nature	Molecular recording of mammalian embryogenesis	GSE117542
Mouse	Endothelial cells	"Cldn5, Cdh5, Hapln1"	Endothelial cells	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Endothelial cells	"Cldn5, Cdh5, Hapln1"	Endothelial cells	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Erythrocytes	"Hemgn, Alas2, Alad, Hbq1b, Hba-x, Hbb-y"	Erythrocytes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Erythrocytes	"Hemgn, Alas2, Alad, Hbq1b, Hba-x, Hbb-y"	Erythrocytes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Megakaryocytes	"Vwf, Ppbp, Pf4"	Megakaryocytes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Megakaryocytes	"Vwf, Ppbp, Pf4"	Megakaryocytes	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Rnf128, Calb2, Gm9866"	Anterior and medial LNP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Gsc, Pitx2, Osr1"	Posterior and medial LNP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Col9a1, Sox9, Flrt2"	Chondroprogenitors	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Cxxc4, Rerg, Tgfb2"	Cells adjacent to fusing Ect	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Hey2, Emx2, Irx3, Irx5, Lef1"	Cells adjacent to surface Ect	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Cxcl14, Lhx8, Dlx5"	Anterior and medial MxP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Shox2, Lhx6, Asb4"	Palatal shelf	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Sox10, Foxd3, Fabp7, Plp1"	Schwann cell progenitors	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Rnf128, Calb2, Gm9866"	Anterior and medial LNP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Gsc, Pitx2, Osr1"	Posterior and medial LNP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Col9a1, Sox9, Flrt2"	Chondroprogenitors	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Cxxc4, Rerg, Tgfb2"	Cells adjacent to fusing Ect	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Hey2, Emx2, Irx3, Irx5, Lef1"	Cells adjacent to surface Ect	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Cxcl14, Lhx8, Dlx5"	Anterior and medial MxP	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Shox2, Lhx6, Asb4"	Palatal shelf	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Mesenchymal cells	"Alx1, Twist1, Msx1, Prrx2, Sox10, Foxd3, Fabp7, Plp1"	Schwann cell progenitors	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Myeloid cells	"Fcgr1, Fcgr3, Fcgr4, Cd200r1, Itgam, Csf1r, Trem2"	Monocytes/macrophages	Tissue	Embryos	31118233	Development	The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution	GSE132462
Mouse	Progenitor cells	Etv2	Haematoendothelial progenitors	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	B cells	Ebf1	B cells	Tissue	Embryos	31221665	Genes Dev	Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia	NA
Mouse	Stromal cells	"Serping1, Ptn, Cxcl14, Des, A2m"	Decidual stromal cells	Tissue	Embryos	31513564	PLOS Biology	Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy	GSE104842
Mouse	Endothelial cells	"Pecam1, Cdh5, Egfl7, Flt1"	Endothelial cells	Tissue	Embryos	31513564	PLOS Biology	Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy	GSE104842
Mouse	Fibroblasts	"Col6a1, Col6a2, Col3a1, Col1a2, Col1a1"	Fibroblasts	Tissue	Embryos	31513564	PLOS Biology	Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy	GSE104842
Mouse	Immune cells	"Ccl9, Ccl4, Cd68, Ly86, Fcgr3, Fcgr1, Cd14, Coro1a, Arhgdib"	Immune cells	Tissue	Embryos	31513564	PLOS Biology	Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy	GSE104842
Mouse	Macrophages	"Adgre1, Aif1"	Macrophages	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Macrophages	"Adgre1, Aif1"	Macrophages	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Macrophages	"C1qa, C1qb, C1qc"	Macrophages	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Erythrocytes	"Alas2, HbA2"	Erythrocytes	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Erythrocytes	"Alas2, HbA2"	Erythrocytes	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Monocytes	"Ccr2, Ly6c2"	Monocytes	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Monocytes	"Ccr2, Ly6c2"	Monocytes	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Neural cells	"En1, Pax2"	Neural crest cells	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Neutrophils	"Ngp, Ly6g"	Neutrophils	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Neutrophils	"Ngp, Ly6g"	Neutrophils	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Osteoblasts	"Dcstamp, Ocstamp, Atp6v0d2, Ctsk, Mmp9"	Osteoblasts	Tissue	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Osteoblasts	"Dcstamp, Ocstamp, Atp6v0d2, Ctsk, Mmp9"	Osteoblasts	NA	Embryos	31907410	Nat Cell Biol	Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair	GSE125088
Mouse	Endoderm cells	"Lamb1, Plat, Sparc"	Parietal endoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endoderm cells	"Lamb1, Plat, Sparc, Bmp2, Pdgfra"	Parietal endoderm	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Isl1, Tcf21"	Pharyngeal endoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endothelial cells	Plvap	Endothelial cells	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Erythrocytes	Gypa	Erythrocytes	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Mesenchymal cells	Tbx5	Mesenchymal cells	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Muscle cells	Myog	Muscle cells	Tissue	Embryos	32427842	Nat Commun	HOX13-dependent chromatin accessibility underlies the transition towards the digit development program	"GSE123482, GSE145657"
Mouse	Endoderm cells	Gata6	Primitive endoderm cells	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Ectoderm cells	"Irx3, Hesx1, Six3"	Rostral neurectoderm	Tissue	Embryos	30787436	Nature	A single-cell molecular map of Mouse gastrulation and early organogenesis	GSE87038
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Nkx2-1"	Thyroid and thymus	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Irx1"	Lung endoderm cells	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Ppy"	Liver endoderm cells	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Pdx1"	Pancreas endoderm cells	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Fabp1"	Small intestine	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Endoderm cells	"Hnf4a, Plau, Ttr, Lefty1, Hhex, Eomes, Foxa1, Otx2, Foxa2, Afp, Rhox5, Trap1a, Xlr3a, Cdkn2a, Hoxb9"	Posterior gut tube	Tissue	Embryos	30959515	Nature	The emergent landscape of the Mouse gut endoderm at single-cell resolution	GSE123046
Mouse	Mesoderm	"Foxf1, Hand1"	Mesoderm	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Notochord cells	"Nog, Lmx1a"	Notochord cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Paraxial mesoderm	"Msgn1, Fgf4"	Paraxial mesoderm	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Germ cells	"Dppa3, Pou5f1"	Primordial germ cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Anterior endoderm cells	Sox2	Anterior endoderm cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Ectoderm cells	"Tfap2a, Gjb3, Dlx5"	Ectoderm cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Epithelial cells	"Epcam, Foxa1, Foxa2, Cxcr4"	Endoderm epithelial cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Endoderm cells	"Cdx1, Cdx2, Cdx4"	Posterior endoderm	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Endothelial cells	"Sox7, Icam2"	Endothelial cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Epithelial cells	EpCAM	Epithelial cells	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Endoderm cells	"Cubn, Apoc2"	Yolk sac endoderm	Tissue	Endoderm cells	33106598	Cell Res	Single-cell patterning and axis characterization in the murine and human definitive endoderm	"CRA003104, HRA000280"
Mouse	Endothelial cells	Myc	Endothelial cells	Tissue	Endothelium	30075129	Cell Stem Cell	Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities	"GSE115618, GSE116718"
Mouse	Enterocytes	"Apoa1, Apoa4, Mttp, Sis"	Enterocytes	Tissue	Enteroid	31756561	Cell Mol Gastroenterol Hepatol	Enteroendocrine Progenitor Cell_Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner	NA
Mouse	Paneth cells	"Defa17, Defa3, Lyz1"	Paneth cells	Tissue	Enteroid	31756561	Cell Mol Gastroenterol Hepatol	Enteroendocrine Progenitor Cell_Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner	NA
Mouse	Progenitor cells	"Cenpa, Lgr5"	Progenitor cells	Tissue	Enteroid	31756561	Cell Mol Gastroenterol Hepatol	Enteroendocrine Progenitor Cell_Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner	NA
Mouse	E3.5 inner cell mass	"Bhmt, AC134841.1, Gm5096, Gm15622, Splc, AA467197, Trim43c, Calcoco2, Pramel6, Gm5612"	E3.5 inner cell mass	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	E6.5 primitive streak	"Aplnr, Mesp1, Mesp2, Pcdh8, Bmp7, Lmo1, Cdh11, Sp5, Foxc2, Lhfp"	E6.5 primitive streak	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Epiblast stem cells	Fgf5	Epiblast stem cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Mesoderm	"Mixl1, Eomes"	Mesoderm	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Pluripotent cells	"Zfp42, Nanog, Pou5f1, Esrrb, Dppa3, Tcf15, Cbx7"	Pluripotent cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Epiblast cells	"Fgf5, Dnmt3b, Pou3f1"	Post-implantation epiblast cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Epiblast cells	"H2-M5, Enox1, Ubd, 2410137M14Rik, Trem2, Gm9732, Gm8127, Notum, Sept1, Manba"	E4.5 epiblast	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Endoderm cells	"Gm13270, Sox7, Tfec, 4930506M07Rik, Lama1, 9930013L23Rik, Htra1, Cyp4f14, Hnf1b, Fam198b"	E4.5 primitive endoderm	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Epiblast cells	"Pla2g1b, Mt3, Hormad1, Alre, BC033916, Tdrd12, Tuba3a, Tmem54, Atox1, Tcea3"	E5.5 epiblast	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Endoderm cells	"Rnase4, Ang, F5, Apob, Fgb, Gm10680, Apoa4, Tmprss2, AC153547.1, Cllc6"	E5.5-6.5 visceral endoderm	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Epiblast cells	"Dpysl2, Nap1l1, Zic5, Npm1, Set, Ncl, Zic2, Pbx1, Rps25, Hnrnpa0"	E6.5 epiblast	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Stem cells	PRC1	Embryonic stem cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Endoderm cells	"Foxa2, Cer1"	Endoderm cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Neural cells	"Nkx6-1, Lhx1, Lhx5"	Neural lineages	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Ectoderm cells	Sox1	Neuroectoderm cells	Cell line	Epiblast stem cells	30118958	Stem Cell Res	A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo	GSE100597
Mouse	Mature osns	Omp	Mature osns	Tissue	Epithelium	33027656	Cell Rep	Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors.	GSE157120
Mouse	Mb	"Mmp12, Mmp13, Spic"	Mb	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cell	"Sfrp5, Cldn10"	Non-ameloblast epithelium cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Si cells	"Ank2, Ccnb1"	Si cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Epithelial cells	"Krt4, Krt13"	Squamous epithelial cells	Tissue	Epithelium	30069044	Nature	A revised airway epithelial hierarchy includes CFTR-expressing ionocytes	GSE103354
Mouse	Tumor cells	"Krt8, Krt16"	Tumor cells	Tissue	Epithelium	30855280	J Clin Invest	Endothelial miR-30c suppresses tumor growth via inhibition of TGF-beta-induced Serpine1	GSE118904
Mouse	Tuft cells	Rgs13	Tuft cells	Tissue	Epithelium	30069044	Nature	A revised airway epithelial hierarchy includes CFTR-expressing ionocytes	GSE103354
Mouse	Ciliated cells	Cdhr3	Ciliated cells	Tissue	Epithelium	30069044	Nature	A revised airway epithelial hierarchy includes CFTR-expressing ionocytes	GSE103354
Mouse	Epithelial cells	"Press16, Ly75, Enpep"	Cortical thymic epithelial cells	Cell line	Epithelium	30968547	Aging Cell	Cell type specific role of lamin B1 in thymus development and its inflammation driven reduction in thymus aging	NA
Mouse	Cycling cells	"Ccnb1, Birc5, Ung, Top2a, Cdc20, Ccnb2"	Cycling cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Endothelial cells	"Pecam1, Vegfr2"	Endothelial cells	Tissue	Epithelium	30855280	J Clin Invest	Endothelial miR-30c suppresses tumor growth via inhibition of TGF-beta-induced Serpine1	GSE118904
Mouse	Fibroblasts	Acta2	Fibroblasts	Tissue	Epithelium	30855280	J Clin Invest	Endothelial miR-30c suppresses tumor growth via inhibition of TGF-beta-induced Serpine1	GSE118904
Mouse	Epithelial cells	"Ccl21a, Ccl21b, Pdpn"	Junctional thymic Epithelial cells	Cell line	Epithelium	30968547	Aging Cell	Cell type specific role of lamin B1 in thymus development and its inflammation driven reduction in thymus aging	NA
Mouse	Immune cells	"Fcer1g, Tyrobp, C1qb, C1qc, Tmsb4, C1qa, B2m, H2-D1, Ftl1, Lyz2"	Immune cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Mesenchymal cells	"Serpinf1, Pcolce, Msx1, Col3a1, Col1a1, Mfap4, Ctsk, Nbl1, Cxcl12, Prrx2"	Mesenchymal cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Ameloblast cells	"Igfbpl1, Ank2"	Pre-ameloblast cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Stem cells	"Sox2, Bmi1, Gli1, Lrig1"	Stem cells	Organoids	Epithelium	31481792	Nat Cell Biol	A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage	GSE131204
Mouse	Macrophages	"Csf1r, Fcgr3, Adgre1, Ms4a7"	Macrophages	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Macrophages	"Mrc1, Cd209f, Cd163"	Macrophages	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Aire, CD40, Cxcl13, II12a, Ccl5"	Medullary thymic Epithelial cells	Cell line	Epithelium	30968547	Aging Cell	Cell type specific role of lamin B1 in thymus development and its inflammation driven reduction in thymus aging	NA
Mouse	Pericytes	"Rgs5, Des, Notch3"	Pericytes	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Enterocytes	ACE2	Enterocytes	Tissue	Epithelium	32404436	Sci Immunol	TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of Human small intestinal enterocytes	GSE149907
Mouse	Goblet cells	Tmprss2	Goblet cells	Tissue	Epithelium	32404436	Sci Immunol	TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of Human small intestinal enterocytes	GSE149907
Mouse	Lymphocyte cells	CD45	Intraepithelial lymphocytes	Tissue	Epithelium	32404436	Sci Immunol	TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of Human small intestinal enterocytes	GSE149907
Mouse	Tuft cells	cd44	Tuft cells	Tissue	Epithelium	32404436	Sci Immunol	TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of Human small intestinal enterocytes	GSE149907
Mouse	Progenitor cells	"Eya1, Plcb2, Myl1, Plet1, Cldn3, Cldn4, Enpep, Pth, Ptn, Pdpn, Lrrc23, Tekt1"	Progenitor cells	Cell line	Epithelium	30968547	Aging Cell	Cell type specific role of lamin B1 in thymus development and its inflammation driven reduction in thymus aging	NA
Mouse	Neural cells	Gap43	Immature olfactory sensory neurons (osns)	Tissue	Epithelium	33027656	Cell Rep	Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors.	GSE157120
Mouse	B cells	"Cd79a, Cd79b"	B cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	CD4 T cells	Cd4	CD4 T cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	CD8 T cells	"Cd8a, Cd8b1"	CD8 T cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Dendritic cells	"Napsa, Traf1, Cd209a, Flt3"	Dendritic cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Epcam, Krt17, Krt14, Krt5, Acta2, Myl9, Mylk, Myh11"	Myoepithelial	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Epcam, Krt19, Krt18, Krt8, Prlr, Pgr, Esr1, Cited1, Prom1"	Luminal HS	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Epcam, Krt19, Krt18, Krt8, Mfge8, Trf, Csn3, Wfdc18, Ltf, Elf5"	Luminal AV	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Epcam, Kit, Aldh1a3, Cd14"	Luminal progenitor	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Epithelial cells	"Epcam, Wap, Glycam1, Olah"	Mature alveolar	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Fibroblasts	"Col1a1, Col1a2, Col3a1, Fn1"	Fibroblasts	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Endothelial cells	"Mmrn1, Prox1, Flt4, Ccl21a"	Lymphatic endothelial cells (LECs)	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Lymphocyte cells	"Cd3d, Cd3e, Cd3g"	Lymphocytes	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Myeloid cells	"Cd74, Lyz2"	Myeloid cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Natural killer (NK) cells	"Gzma, Ncr1, Itgae"	Natural killer (NK) cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Endothelial cells	"Sox17, Sele"	Vascular endothelial cells	Tissue	Epithelium	33378681	Cell Rep	Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing	GSE150580
Mouse	Early retinal precursor cells	"Top2a, Ube2c"	Early retinal precursor cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Late retinal precursor cells	"Top2a, Ube2c"	Late retinal precursor cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Maturation	"CXCR2, S100a8"	Maturation	Tissue	Eye	33106668	Nat Immunol	A new neutrophil subset promotes CNS neuron survival and axon regeneration	GSE144637
Mouse	Multipotent rpcs	"Vsx2, Hes1, Nr2e1"	Multipotent rpcs	Cell line	Eye	31260032	Invest Ophthalmol Vis Sci	Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors	GSE132272
Mouse	Neurogenic cells	"Top2a, Ube2c, Atoh7, Olig2"	Neurogenic	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Neurogenic cells	"Olig2, Neurog2, Otx2, Atoh7"	Neurogenic rpcs	Cell line	Eye	31260032	Invest Ophthalmol Vis Sci	Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors	GSE132272
Mouse	Photoreceptors	Olig2	Photoreceptor precursors	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Ganglion cells	"Atoh7, Pou4f2"	Retinal ganglion cell (rgc)/amacrine (ac) rpcs	Cell line	Eye	31260032	Invest Ophthalmol Vis Sci	Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors	GSE132272
Mouse	Ganglion cells	"Bco2, Mmp2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Fmo1, lhx9"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Fst	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Kcns1, Mmp14, Cys1, Tusc5"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Egln3, Sostdc1"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Cav1, Pdlim5, Chrdl1"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Pde1a	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Wisp1, Tg, Cgh9, C1ql2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Pip5k1b, Slc7a11"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Pkib	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Prps2, Stxbp6, Tpbgl"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Adgrl2, Arhgap31"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Col12a1, Amigo2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Jam2	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Bend4, Wnt11, Cmbl"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Creb3l2	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Nek7	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Gm13111, Adam7"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Uts2b, Esrrb, Anxa11, Lims2, AdamtS5"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Kcng1, Arghef26, Vcan, Kcns3"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Serpinb12, Fes, Gpx6, NetO1"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Krt81, Tgfb3, Fgd2, Nab2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Adora2a, Chrnb4, Adgrg6, Tiparp"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Prox1, Prox1os, Cha1, Runx2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Gna14	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Eya2	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Runx1	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Plpp3, Nfia, Gas1"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Fam19A4	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Vit	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Trhr	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Npy	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Mybpc3, Guca1b, Tff3, Il1rapl2"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Zic1	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Ptpn22, Gm26612, Itgb5, Ttn"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Frk, Tnfrsf11b, Hs3st3b1"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Sntn, GM11100, Etnppl, Stra6"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	Erbb4	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Crisp1, GM2115, Tnc, Crh, Rph3al"	Retinal ganglion cells sub1	Tissue	Eye	30018341	Nat Commun	Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes	GSE115404
Mouse	Ganglion cells	"Pou4f2, Rbpms"	Retinal ganglion cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Epithelial cell	"Rpe65, Rlbp1"	Retina pigment epithelium	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Rods	"Nrl, Rho, Crb1-B, Gnat1"	Rods	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Bipolar cells	"Bhlhe23, Grm6, Pcp2"	Bipolar cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Cones	"Thrb, Rxrg, Gngt2, Gnb3"	Cone photoreceptors	Cell line	Eye	31260032	Invest Ophthalmol Vis Sci	Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors	GSE132272
Mouse	Cones	"Gnat2, Opn1sw"	Cones	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Hematopoietic cells	Ptprc	Hematopoietic cells	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Horizontal cells	Lhx1	Horizontal cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Melanocytes	"Pmel, Mlana"	Melanocytes	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Muller cells	"Crb1-A, Aqp4, Clu"	Muller glia cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Neutrophils	Mrc	Alternative activated neutrophils	Tissue	Eye	33106668	Nat Immunol	A new neutrophil subset promotes CNS neuron survival and axon regeneration	GSE144637
Mouse	Endothelial cells	"Cdh5, Pecam1, Flt1, Cldn5, Kdr, Vwf"	Endothelial cells	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Muscle cells	"Cspg4, Acta2, Myh11, Pmel"	Smooth muscle cells	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Stromal cells	"Pdgfra, Pdgfrb, Col1a1"	Stromal cells	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Amacrine cells	"Slc18a3, Tfap2a"	Amacrine cells	Organoids	Eye	32620864	Nat Commun	Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease	PRJNA547800
Mouse	Schwann cells	"Mbp, Mag, Mpz"	Schwann cells	Tissue	Eye	32196081	Journal of Experimental Medicine	Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid	GSE95835
Mouse	Ci2c-like cells	"Zscan4, Oct4, Tcstv1, Dppa"	Ci2c-like cells	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	Cipscs	"Nanog, Sox17"	Cipscs	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	Further reprogrammed cells in stage ii and iii	"Zscan4, Tcstv1"	Further reprogrammed cells in stage ii and iii	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	Mefs	"Prrx1, Twist2, Zeb2, Thy1, Fbn1"	Mefs	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	Reprogrammed cells in stage i	"Gata4, Gata6, Sox17, Foxa2, Epcam, Epcam"	Reprogrammed cells in stage i	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	Xen-like cells	"Sox17, Sall4, Gata4, Gata6"	Xen-like cells	Tissue	Embros	29937202	Cell Stem Cell	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming	GSE45719
Mouse	B cells	Cd19	B cells	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Pecam1, Cdh5, Cd34"	Endothelial cells	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Myeloid cells	"Itgam, Cd68, C1qa, Lyz2, Cd14"	Myeloid cells	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer (NK) cells	"Irf8, Gzma, Nkg7"	Natural killer (NK) cells	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Progenitor cells	"Pdgfra, Cd34"	Mesenchymal progenitors	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	"Cd3g, Cd8a, Cd4"	T cells	Tissue	Fat	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Pericytes	Mcam	Pericytes	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Macrophages	"CD45, CD206"	M2 macrophages	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Red cells	"Hba-a1, Hba-a2, Hbb-bt"	Red blood cells	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Endothelial cells	CD31	Endothelial cells	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Neural cells	"Plp1, Prx"	Nerve cells 1	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Neural cells	"Ncam1, Lgi4"	Nerve cells 2	Tissue	Foot	32877217	Am J Physiol Cell Physiol	Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons	GSE138515
Mouse	Reactive microglia	Il1a	Reactive microglia	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Astrocytes	Gja1	Astrocytes	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Endothelial cells	Flt1	Endothelial cells	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Slc17a7	Excitatory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Slc17a7	Excitatory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Slc17a7	Excitatory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Gad2	Inhibitory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Gad2	Inhibitory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Gad2	Inhibitory neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Microglia cells	C1qa	Microglia cells	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Snap25	Neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Snap25	Neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Neural cells	Snap25	Neurons	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Oligodendrocytes	Bmp4	Newly formed oligodendrocytes	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Oligodendrocytes	Pdgfra	Oligodendrocyte precursors	Tissue	Frontal cortex	31519873	Nat Commun	Cell type-specific transcriptional programs in Mouse prefrontal cortex during adolescence and addiction	GSE124952
Mouse	Astrocytes	Aldoc	Astrocytes	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Endothelial cells	Cldn5	Endothelial cells	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Neural cells	Igfbpl1	Interneurons	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Oligodendrocytes	Mbp	Mature oligodendrocytes	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Microglia cells	Aif1	Microglia cells	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Oligodendrocytes	Olig2	Oligodendrocytes	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Neural cells	CamK2a	Pyramidal neurons	Tissue	Frontal cortex	31606247	Neuron	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mouse	GSE123652
Mouse	Neural cells	"Foxp2, Tle4, Ephb1"	L6 CThPNs	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	"Trhr, Tshz2"	L5 near-projecting neurons (NPNs)	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	"Mdga1, Pou3f1"	L2/3 IT	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	"Rou3f1, Rorb"	L2/5 IT	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Oprk1	L6 ITPNs	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Htr3a	5-HT3R	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Lamp5	LAMP5	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Sst	SST	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Cdca7	Mig.INT	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	Lhx5	CR	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	"Htr3a, Lamp5, Sst"	Interneurons	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Neural cells	"Cdca7, Sp9"	Migrating cortical interneurons	Tissue	Frontal cortex	31711176	Cerebral Cortex	Cortical_oxp2_upports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression	GSE130653
Mouse	Tumor cells	"Ube2c, Gal, Top2a"	Tumor cells1	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Tumor cells	"Bgn, MT2, Meg3"	Tumor cells2	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Tumor cells	"Grp, Tslp"	Tumor cells3	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Dendritic cells	"Ccl17, Ccl22, Ccr7"	Dendritic cells	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Endothelial cells	"Igfbp7, Ctla2a, Col4a1"	Endothelial cells	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Fibroblasts	"Col1a1, Mfap5, Mgp"	Fibroblasts	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Muscle cells	"Mylpf, Ttn, Acta1"	Muscle cells	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Myeloid cells	"Mki67, Hist1h2ap"	Myeloid1	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Myeloid cells	"Ly6c2, Plac8, Ms4a4c"	Myeloid2	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Myeloid cells	"Apoe, Pf4, Ccl6"	Myeloid3	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Myeloid cells	"H2-Eb1, H2-Ab1"	Myeloid4	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Myofibroblasts	"Higd1b, Rgs5"	Myofibroblasts	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Neutrophils	"S100a9, Il1b, S100a8"	Neutrophils	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Plasmacytoid dentritic cells	"Igkc, Ly6d, Ighm"	Plasmacytoid dentritic cells	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	T cells	"Gzma, Nkg7, Ms4a4b"	T cells	NA	Gastrocnemius muscle	31462499	Proc Natl Acad Sci U S A	Neutrophils promote tumor resistance to radiation therapy	NA
Mouse	Endothelial cells	"Cdh5, Tie1"	Endothelium	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Head mesenchyme	"Olfr129, Onecut1"	Head mesenchyme	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Heart	"Hand2, Gata6"	Heart	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Presomitic mesoderm	"Hes7, Tbx6"	Presomitic mesoderm	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Somite	"Aldh1a2, Uncx4.1"	Somite	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Differentiated cells	"Meox2, Pax3"	Differentiated somite	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Differentiated cells	"Lfng, Mesp2, Ripply2, Dll1"	Differentiation front	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Endoderm cells	"Col4a1, Epcam, Sox17"	Endoderm cells	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Endothelial cells	Etv2	Haemato-endothelial progenitors	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Endothelial cells	Kdr	Haemato-endothelial progenitors and endothelium	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Allantois	"Tbx4, Hoxa11, Ass1, Bmp7"	Allantois	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Neural cells	"Pax6, Sox1, Hes3, Sox2"	Differentiated neural cells	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Ectoderm cells	"Ephx2, Mt1, Utf1, Pou5f1"	Primordial-germ-cell-like or extra-embryonic ectoderm	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Progenitor cells	"Wnt3a, Fgf17, Fgf8, Cyp26a1, Nkx1-2"	Tail bud containing neuromesodermal progenitors	Tissue	Gastruloids	32076263	Nature	Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids	GSE123187
Mouse	Double-positive cells	CD14	Double-positive cells	Tissue	Gland	29158510	Nat Commun	Construction of developmental lineage relationships in the Mouse mammary gland by single-cell RNA profiling	GSE103275
Mouse	Hormone sensing differentiated	"Esr1, Prlr, Pgr, S100a6, Cited1"	Hormone sensing differentiated	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Hormone_x005f_x0002_responsive luminal (l-hr) cells	Prlr	Hormone_x005f_x0002_responsive luminal (l-hr) cells	Organoids	Gland	33086071	Cell Rep	Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity	GSE157890
Mouse	Pericytes	"Des, Cspg4"	Pericyte cells	Cell line	Gland	32930441	Stem Cells	Single-cell profiling of long noncoding RNAs and their cell lineage commitment roles via RNA-DNA-DNA triplex formation in mammary epithelium	NA
Mouse	Stem cells	"Procr, Lgfbp4, Gng11, Zeb2"	Procr stem cells	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Stem cells	"Procr, Gng11, Zeb2, Cdh5"	Procr stem cells	Tissue	Gland	33382976	Stem Cell Reports	AP-2gamma Is Required for Maintenance of Multipotent Mammary Stem Cells.	GSE143159
Mouse	Secretory cells	Kit	Secretory luminal (l-sec) cells	Organoids	Gland	33086071	Cell Rep	Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity	GSE157890
Mouse	Basal cells	"Krt4, Krt14, Pdpn, Etv5, Acta2"	Basal cells	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Myoepithelial cells	"Oxtr, Acta2, Krt4, Krt14"	Myoepithelial cells	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Alveolar cells	Creb3l2	Alveolar cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Alveolar cells	"Cd14, Csn3, Krt8"	Alveolar precursors	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Basal cells	"Itgb1, Krt14"	Basal cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Basal cells	"Epcam, Cd49f"	Basal cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Basal cells	Ehf	Basal cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	B cells	Cd74	B cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Basal cells	"Cd49f, Krt14, Krt5, Krt17"	Basal cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Esam, Pecam1"	Endothelial cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Stromal cells	"Vim, Fn1"	Stromal cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Differentiated cells	"Wap, Csn2, Glycam1, Lalba"	Differentiated alveolar cells	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Progenitor cells	CD55	Early progenitor cells	Tissue	Gland	29158510	Nat Commun	Construction of developmental lineage relationships in the Mouse mammary gland by single-cell RNA profiling	GSE103275
Mouse	Epithelial cells	"Trim29, Vim, Cldn6, Sox4"	Epithelial mesenchymal transition like cells	Tissue	Gland	33120014	Dev Cell	Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors	GSE158257
Mouse	Fibrocytes	Col1a1	Fibrocytes	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Progenitor cells	"Esr1, Prlr, Pgr, S100a6, Cited1, Aldh1a3, Cd14 , Kit"	Hormone sensing progenitors	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Luminal cells	"Atf4, Cebpd, Cebpb, Yy1"	ER+ luminal cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Luminal cells	"Cd24, Krt8, Krt18, Krt19"	Luminal cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Luminal cells	"Cd24, Krt8, Krt18, Krt19"	Luminal cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	"Krt18, Krt19, Epcam"	Luminal epithelial cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Epithelial cells	"Krt18, Krt19, Epcam"	Luminal epithelial cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Luminal cells	"Pgr, Prlr, Foxa1, Gpx3, Esr1"	Luminal mature cells	Tissue	Gland	33120014	Dev Cell	Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors	GSE158257
Mouse	Luminal cells	"Aldh1a3, Cd14, Kit"	Luminal progenitors	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	Luminal cells	"CD14, Kit, Lalba"	Luminal progenitors	Tissue	Gland	33120014	Dev Cell	Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors	GSE158257
Mouse	Luminal cells	"Aldh1a3, Kit, Cd14, Krt18"	Luminal progenitors	Tissue	Gland	33382976	Stem Cell Reports	AP-2gamma Is Required for Maintenance of Multipotent Mammary Stem Cells.	GSE143159
Mouse	Macrophages	"Cd74, Cd14, Csf1r"	Macrophages	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	Fcgr1	Macrophages	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	B cells	Cd19	B cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Basal cells	"Acta2, Krt14, Krt5, Mylk, Myl9, Tagln"	Basal cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Dendritic cells	Cd24a	Dendritic cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Endothelial cells	"Id1, Pecam1, Egfl7, Apold1, Plvap, Lrg1, Fabp4"	Endothelial cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Fibroblasts	"Col1a1, Col1a2, Col6a1, Mmp2, Tnxb"	Fibroblasts	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Natural killer (NK) cells	Klrb1c	Natural killer (NK) cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	Macrophages	"Cd68, Csf1r, Cd14, Mafb"	Macrophages	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Macrophages	"Cd14, Retnla, Cd68, Cd163, C1qb"	Macrophages	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Luminal cells	"Ly6a, Krt8"	Mature luminal cells	Tissue	Gland	30089273	Cell Rep	Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development	GSE111113
Mouse	Luminal cells	"Esr1, Pgr, Prlr, Epcam"	Mature luminal cells	Tissue	Gland	33382976	Stem Cell Reports	AP-2gamma Is Required for Maintenance of Multipotent Mammary Stem Cells.	GSE143159
Mouse	T cells	"Cd3d, Lef1, Crem"	Memory T cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	T cells	NA	Naive T cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	T cells	"Cd3d, Lef1, Sell"	Naive T cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	B cells	"Igkc, Ms4a1"	B cells	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Dendritic cells	"Ccl22, Xcr1"	Dendritic cells	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Epithelial cells	"Prlr, Krt18"	Epithelial cells	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Endothelial cells	Lyve-1	Lymphatic endothelial cells (LECs)	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Monocytes	Ly6c2	Monocytes	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Natural killer (NK) cells	"Ncr1, Nkg7"	Natural killer (NK) cells	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Progenitor cells	"Wap, Csn2, Glycam1, Lalba, Aldh1a3, Cd14, Kit"	Progenitor alveolar cells	Tissue	Gland	29225342	Nat Commun	Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing	GSE106273
Mouse	B cells	Cd79a	B cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Dendritic cells	Siglech	Dendritic cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Dendritic cells	"Cd14, Clec4e"	Dermal dendritic cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Monocytes	"Cd14, Tnip3, Retnla, Cd68"	Monocytes	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Natural killer (NK) cells	"Gzma, Nkg7"	Natural killer (NK) cells	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Fibroblasts	Vim	Stromal fibroblasts	Tissue	Gland	32785175	Cancers (Basel)	Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland Microenvironment	GSE152866
Mouse	Endothelial cells	"Eng, S1pr1, Emcn"	Endothelial cells	Cell line	Gland	32930441	Stem Cells	Single-cell profiling of long noncoding RNAs and their cell lineage commitment roles via RNA-DNA-DNA triplex formation in mammary epithelium	NA
Mouse	Epithelial cells	"Cd24a, Cd29, Krt14, Krt18"	Epithelial cells	Cell line	Gland	32930441	Stem Cells	Single-cell profiling of long noncoding RNAs and their cell lineage commitment roles via RNA-DNA-DNA triplex formation in mammary epithelium	NA
Mouse	Immune cells	"Cd74, Cd72, Cd54"	Immune cells	Cell line	Gland	32930441	Stem Cells	Single-cell profiling of long noncoding RNAs and their cell lineage commitment roles via RNA-DNA-DNA triplex formation in mammary epithelium	NA
Mouse	T cells	Cd3	T cells	Tissue	Gland	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	"Cd3e, Gata3"	T cells	Tissue	Gland	31701034	Commun Biol	Single-cell RNA-sequencing analysis of estrogenand endocrine-disrupting chemical-induced reorganization of Mouse mammary gland	GSE125272
Mouse	T cells	"Cd3d, Cd8b1"	T cells	Tissue	Gland	32479261	eLife	Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous Mouse	GSE148209
Mouse	Basal cells	Krt14	Basal cells	Organoids	Gland	33086071	Cell Rep	Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity	GSE157890
Mouse	Basal cells	"Krt14, Krt5, Snai2"	Basal cells	Tissue	Gland	33120014	Dev Cell	Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors	GSE158257
Mouse	Basal cells	"Krt14, Krt8, CD14"	Lumino-basal cells	Tissue	Gland	33120014	Dev Cell	Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors	GSE158257
Mouse	Basal cells	"Krt5, Krt14, Acta2, Cre"	Basal cells	Tissue	Gland	33382976	Stem Cell Reports	AP-2gamma Is Required for Maintenance of Multipotent Mammary Stem Cells.	GSE143159
Mouse	Chief cells	Pgc	Chief cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Deep mucous cells	"Gif, Itln1"	Deep mucous cells	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Gastric corpus metaplasia cells	Gkn3	Gastric corpus metaplasia cells	Tissue	Gut	32835664	Gastroenterology	Single-Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric Corpus	NA
Mouse	Stem cells	"Lgr5, Axin2, Sox9"	Gastric stem cells	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Mucous cells	Muc6	Gland mucous cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Intestinal cells	"Muc2, Cdx1"	Intestinal lineage	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Lgr5pos cells	"Muc6, Pgc, Gif, Aqp5, Gkn3, Clcn3, Pbx1"	Cluster1	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	"Sprr2a1, Sptssb, Gkn2, Gsta1, Sprr2a3, Sppr2b"	Cluster2	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	"Srprk2, Lmo2, Sprr1a, Ifrd1, Erdr, Chka"	Cluster3	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	"Atp4a, Chia1"	Cluster4	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	NS	Cluster5	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	"Muc6, Pgc, Gif, Aqp5, Gkn3"	Infected-Cluster1	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	"Sprr2a1, Gkn2, Gsta4, Sprr2a3, Sppr2b"	Infected-Cluster2	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	Cfap69	Infected-Cluster3	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	Apoa1	Infected-Cluster4	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Lgr5pos cells	Dclk1	Infected-Cluster5	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Mucous cells	Muc5ac	Mucous cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Mucous cells	Muc5ac	Mucous cells	Tissue	Gut	31235935	Nat Cell Biol	"R-spondin-3 induces secretory, antimicrobial Lgr5 + cells in the stomach"	GSE124930
Mouse	Parietal cells	Atp4b	Parietal cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Cell cycling cells	"AU040972, Hmgb2, Birc5, Smc5, Ube2c, Cdca3, H2afz, Cenpa, Stmn1, Top2a, Cdc20, Cks1b, Cdk1, Cenpf, Pttg1, Tuba1b, Smc2, 2810417H13Rik, 2700094K13Rik, Lgals1, Tubb5"	Cell cycling cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	B cells	"Cd79a, Cd79b, Ms4a1"	B cells	Tissue	Gut	30173915	Cell	Self-Maintaining Gut Macrophages Are Essential for Intestinal Homeostasis	NA
Mouse	Paneth cells	"Itln1, Defa"	Paneth cells	Tissue	Gut	30173915	Cell	Self-Maintaining Gut Macrophages Are Essential for Intestinal Homeostasis	NA
Mouse	Ciliated cells	"Hmgb2, Elof1, Chchd10, Ift172, 1700016K19Rik, Cfap126, Tppp3, Ccdc153, Tmem212, Pifo, Mlf1, Meig1, 1700007K13Rik, Fam183b, Rsph1"	Ciliated cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Basal cells	"Krt5, Hspb1, Krt14, Ecm1, Hspb8, Sfn, Fxyd3, Lmo1, Perp, Urah, Krt17, Mt2, Hcar2, Mt1, Ly6a"	Basal cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Epithelial cells	"Elof1, Chchd10, Ift172, 1700016K19Rik, Cfap126, Tppp3, Ccdc153, 1700088E04Rik, Tmem212, Pifo, Mlf1, Meig1, Lrrc51, 1700007K13Rik, Fam183b, Tmem107, Ift43, Ccdc189, Rsph1, Arhgdig, 1110004E09Rik, Prr29, Tctex1d4, Cfap206, Spef1, 2410004P03Rik, AU040972, Bo"	Epithelial cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Fibroblasts	"Sparc, Col3a1, Lgals1, Bgn, Igfbp7, Col1a1, Vim, Serpinh1, Serpinf1, Rcn3, Col1a2, Aebp1, B2m, Selm, Cst3, Cald1, Id3, Col5a2, Mxra8, Timp1, Pcolce, Cpxm1, Cd302, Mfap2, Fbln2, Dcn, Wbp5, Timp2, Tceal8, Efemp2, Ctsz, Ctla2a, Nsg1, Loxl1, Eva1b, Cxcl12, Ig"	Fibroblasts	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Myofibroblasts	"Acta2, Postn"	Myofibroblasts	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Fibroblasts	"Stmn1, Tuba1b, Ccnb1, Smc2, Ccna2, Birc5, Cdca8, Cenpa, Ube2c, Cks1b, Spc24, Cdca3, Pbk, 2810417H13Rik, Cdc20, Lockd, Ccnb2, 2700094K13Rik, Cenpm, Cenpw, Pttg1, Lgals1, Ckap2, Cdk1, Tubb5, Tpx2, Ube2t, Racgap1, Aurka, Cks2, Spc25, Knstrn, Cenpf, Fam64a, C"	Proliferating fibroblasts	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Stem cells	Lgr5	Stem cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Epithelial cells	"Krt5, Hspb1, Krt14, Ecm1, Hspb8, Sfn, Fxyd3, Lmo1, Ucp2, Perp, Urah, Krt17, Ociad2, Mt2, Hcar2, S100a10, Glul, Palmd, Cat, Mt1, Vsnl1, Pycard, Rab27b, Ly6a, Dusp6, App, Lgals3, Ifitm10, Anxa3, Pitx1, Phlda3, Hbegf, Serpinb5, Sostdc1, Anxa1, Gpx2, Anxa8, S"	Epithelial(basal) cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Epithelial cells	"Ly6d, Gsta4, Wfdc2, Epcam, Spint2, Krt7, Fxyd3, Krt19, Eif3f, Cyp2f2, Gsto1, Sfn, Clu, Klf5, Avpi1, S100a14, Rab25, Krt8, Bcam, Perp, Cd24a, Cldn7, Sprr1a, Fam3c, Foxq1, S100a16, Ezr, Anxa8, Gpx2, Pthlh, Lmo7, Cd9, Ahr, Areg, Krt18, Ces1d, Ywhaq, Aqp5, Kr"	Epithelial(ciliated) cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Macrophages	"Ptprc, Cd68, Cd11b, Cd18, Cd45"	Macrophages	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Macrophages	"Cd68, Cx3cr1, Fcgr1, Adgre1, Cd63"	Pan macrophages	Tissue	Gut	30173915	Cell	Self-Maintaining Gut Macrophages Are Essential for Intestinal Homeostasis	NA
Mouse	Epithelial cells	"Hmgb2, Birc5, Smc4, Ube2c, Cdca3, H2afz, Cenpa, Ccna2, Stmn1, Top2a, Cdc20, Cks1b, Cdk1, Nusap1, Cenpf, Cenpe, Pttg1, Ccnb1, Esco2, H2afv, Knstrn, Arl6ip1, Spc24, Mki67, Prc1, Ect2, 2810417H13Rik, Ccdc34, Cdca8, Ccnb2, Pbk, Tpx2, Aurkb, Hmgb1, Tacc3, Racg"	Proliferating epithelial cells	Organoids	Gut	30872643	Sci Rep	Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model	SRP104455
Mouse	Neural cells	"Tubb3, Nefl, Kcnc3, Scn4b"	Spiral ganglion neurons type i	Tissue	Hair	30078710	Cell	Hair Cell Mechanotransduction Regulates Spontaneous Activity and Spiral Ganglion Subtype Specification in the Auditory System	GSE114759
Mouse	Neural cells	Grm8	Spiral ganglion neurons type IA	Tissue	Hair	30078710	Cell	Hair Cell Mechanotransduction Regulates Spontaneous Activity and Spiral Ganglion Subtype Specification in the Auditory System	GSE114759
Mouse	Neural cells	"Prph, Gata3, Mafb, Th"	Spiral ganglion neurons type ii	Tissue	Hair	30078710	Cell	Hair Cell Mechanotransduction Regulates Spontaneous Activity and Spiral Ganglion Subtype Specification in the Auditory System	GSE114759
Mouse	Neural cells	Ngfr	Spiral ganglion neurons type ii	Tissue	Hair	30078710	Cell	Hair Cell Mechanotransduction Regulates Spontaneous Activity and Spiral Ganglion Subtype Specification in the Auditory System	GSE114759
Mouse	Ng2 cells	Pdgfra	Ng2 cells	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Pacemaker cells	Nms	Pacemaker cells	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Suprachiasmatic nucleus neuron	"Avp, Vip, Nms, Cck, C1ql3, Grp, Bdnf, Irs4"	Suprachiasmatic nucleus neuron	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Tanycytes	Col23a1	Tanycytes	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Ependymal cells	Tmem212	Ependymal cells	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Astrocytes	Agt	Astrocytes	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Endothelial cells	Itm2a	Endothelial cells	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Microglia cells	Hexb	Microglia cells	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Neural cells	Celf4	Neurons	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Oligodendrocytes	Plp1	Oligodendrocytes	Tissue	Head	32066983	Nat Neurosci	Spatiotemporal single-cell analysis of gene expression in the Mouse suprachiasmatic nucleus	"GSE117295, GSE118403, GSE132608"
Mouse	Cardiogenic population in sca1+	"Sca1, pdgfra"	Cardiogenic population in sca1+	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Cardiomyopathy	Tnnt2	Cardiomyopathy	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Cm	Top2a	Cm	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-atrial	Kcna5	Cm-atrial	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-avc	Oprk1	Cm-avc	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-lsv	Irx2	Cm-lsv	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-lv	Wdr93	Cm-lv	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-oft	Mybpc1	Cm-oft	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cm-ra	Shox2	Cm-ra	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cms	"Myh6, Nppa"	Cms	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Compact avn cells	"Cx30.2, Cx45"	Compact avn cells	Tissue	Heart	30765799	Sci Rep	Using Gjd3-CreEGFP Mouse to examine atrioventricular node morphology and composition	GSE118932
Mouse	Cp1	Crabp1	Cp1	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cp2	Foxf1	Cp2	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Cp3	Tgfb1	Cp3	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Early icm	"Cxcl1, Plk2"	Early icm	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Ecs	Cxcl16	Ecs	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Epi/endo	"Mmp3, Figf"	Epi/endo	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Epicardium cells	"Tbx18, Mab21l2, Wt1, Hand1, Tcf21, Hand2"	Epicardium cells	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Epicardium cells	"Clu, Dmkn"	Epicardium cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	First heart field	"Nkx2-5, Tbx5, Hcn4"	First heart field	Organoids	Heart	33176168	Cell Stem Cell	Capturing Cardiogenesis in Gastruloids.	GSE158999
Mouse	GATA1 cells	Gata1	GATA1 cells	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	T cells	"Il23r, Trgv2, Il-17a"	IL-17a gamma delta T cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	T cells	"Birc5, Top2a"	IL-17a neg gamma delta T cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Immature cardiomyocytes (hand2osl low)	"Pparg, Cd36, Fli1, Sema6a, Kitl, Ptprb, Nav3, Tspan13, Efr3b, Prkch, Rasgrf2, Ptprg, Spata13, Myo10, Sybu, Shank3, Arhgap31, Lims2, Podxl, Nrp2, Pkp4, Itga6, Zbtb46, Adgrl2, Apbb2, Lnx1, Flt1, Adamts9, Mcf2l, Cdh5, Pdgfd, Ets1, Ablim3, Ccdc85a, Mgll, Ptpr"	Immature cardiomyocytes (hand2osl low)	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Inflammatory cells	Hif1a	Inflammation-associated cell	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Late icm	"Tnni3, Myl7"	Late icm	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Lateral plate mesoderm	"Hand1, Foxf1, Hoxb6, Bmp4, Cfc1, Pitx2"	Lateral plate mesoderm	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Mature cardiomyocytes	"Corin, Fhl2, Rbfox1, Myl2, Jph2, Trdn, Grm1, Mypn, Myocd, Ryr2, Ckmt2, Pde4d, Ldb3, Enah, Myom1, Cdh2, Pip5k1b, Sorbs1, Tnnt2, Esrrg, Kcnj3, Grb14, Itgb6, Pde4b, Pcdh7, Ppargc1a, Fgf13, Sorbs2, Mlip, Alpk2, Fhod3, Pde4dip, Nexn, Rcan2, Cpeb3, Magi2, Tnni3"	Mature cardiomyocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Mes	Rtn1	Mes	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Stem cells	"CD105, CD73, CD44, CD29, Scai, CD45, W8B2"	Mesenchymal stem cells	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Stem cells	Sca1	Mesenchymal stem cells	Tissue	Heart	31359001	Nat Med	Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.	GSE131778
Mouse	Stem cells	"Nt5e, Eng"	Mesenchymal stem cells	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	Mesothelial cells	"Kcnn3, Efnb2, Cp, Prox1, Ppfibp1, Slfn3, Sema6a, Lama4, Flt4, Nxn, Ntn1, Tc2n, Zfp521, Sncaip, Klhl4, Nrp2, Kif26b, Ptpn14, Prkcq, Tspan18, Sema3a, Prkag2, Prkcz, D5Ertd615e, Srgap3, Apba2, Sh3gl3, Gpm6a, Thsd4, Dapk2, Abi3bp, Fmnl2, Stox2, Galnt18, Pkhd1"	Mesothelial cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Modsmc	"Fn1, Mgp, Nupr1, Eln, Igfbp2, Tnfrsf11b"	Modsmc	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Modulated smc	"Tagln, Cnn1, Lgals3, FN1, Tnfrsf11b, Col1alpha1"	Modulated smc	Tissue	Heart	31359001	Nat Med	Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.	GSE131778
Mouse	Monoblasts	"Celf2, Axl, Bicc1, Eya2, Lama2, Dcn, Igf1, Egfr, Gfpt2, Abca8b, Vcan, Scara5, Ebf2, Sdc2, Enpp2, Shank3, Fstl1, Adamts5, Fkbp5, Zeb1, Lims2, Lvrn, Papss2, Col5a2, Lamc1, Eng, Gsn, Fbn1, Epha7, Col15a1, Htra3, Pdgfra, Flt1, Pcsk6, Gpm6b, Vegfc, Tenm3, Gnao"	Monoblasts	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Mural cells	"Cspg4, Pdgfrb"	Mural cells	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Myocardial	"Myh7, Myl4, Tnnc1, Tnnt2, Myl2"	Myocardial	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Myocardium	"Stard10, Kcna5, Vsnl1, Cav1, Nr2f2, Angpt1, Nppa"	Atria	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Myocardium	"Rspo3, Msx2, Tbx2, Tbx5, Vsnl1, Bmp2, Hand1"	Atrioventricular canal	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Myocardium	"Fhl1, Rgs5, Isl1, Tdgf1, Wnt5a, Sema3c, Hand2, Bmp4, Pitx2, Rspo3"	Outflow Tract	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Myocardium	"Shox2, Nr2f2, Wnt2, Vsnl1, Mab21l2, Tbx5"	Sinus Venosus	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Myocardium	"Myl2, Nppa, Myh7, Irx4, Hey2, Nppb, Cited1"	Ventricle	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Myocytes	Actn2	Myocytes	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	NA	"Sox17, Stmn2"	"EC1, arteriole"	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	NA	"Cd300lg, Ramp3"	"EC2, capillary"	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	NA	"Emcn, Vwf"	"EC3, venule"	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	NA	"Flt4, Mmrn1"	"EC4, lymphatics"	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	NA	"Cxcr6, Icos, Cd3g, Il7r"	CXCR6+ T cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	NA	"Cd8a, Cd8b1, Nkg7"	CD8+ T cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	NA	NA	"Bmx, Sema3g, Efnb2, Sox17, Hey1"	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	NA	"Nr2f2, Vwf"	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	"Cd4, Lef1"	TC2- Cd4	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	"Mgl2, Cbr2, Folr2"	MAC-TR	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	"Cxcl10, Rsad2, Ifit3, Ifit1, Ifi47"	MAC-IFNIC	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	"Retnlg, G0s2, Lcn2, Wfdc21, Pglyrp1"	MAC6	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	"Ear2, Eno3 Itgal Ace"	MAC7	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	NA	Saa3 Ltc4s	MAC8	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Nodal-ventricular (n-v) transitional cells	Myl2	Nodal-ventricular (n-v) transitional cells	Tissue	Heart	30765799	Sci Rep	Using Gjd3-CreEGFP Mouse to examine atrioventricular node morphology and composition	GSE118932
Mouse	Paraxial mesoderm	"Fst, Tcf15, Meox1, Foxc2, Foxd1, Foxc1"	Paraxial mesoderm	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Pericardial	"Upk3b, Msln, Myl7, Igfbp6, Igfbp5"	Pericardial	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Cardiomyocytes	"Kif23, Mis18bp1, Prc1, Mki67, Top2a"	Proliferative cardiomyocytes	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Second heart field	"Tbx1, Isl1, Fgf10"	Second heart field	Organoids	Heart	33176168	Cell Stem Cell	Capturing Cardiogenesis in Gastruloids.	GSE158999
Mouse	Sinoatrial node	"Isl1, Tbx18, Hcn4, Tbx3, Bmp4, Smoc2"	Sinoatrial node	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Sinoatrial node head	"Smoc2, Tmsb4x, Meg3, Nrk, Egr1, Isl1, Bmp4, Sfrp1, Cited1, Sparc, Acta2, Sulf2, Mdk, H19, Lbh"	Sinoatrial node head	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Sinoatrial node junction	"Acvr1c, Cpne5, Nr2f1, Slc22a1, Peg3, Palld, Fst, Tbx20, Pam, Id2, Nr2f2, Gm42418, Ccnd2, Cldn11, Epha4"	Sinoatrial node junction	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Muscle cells	"Cnn1, Acta2, Tagln2, Tagln"	Smooth muscle_pericyte-like cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	T-helper 17 cells	"Tnfsf8, Cxcr6, Cd4, Il17a, Rora"	T-helper 17 cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	T-natural killer	"Nkg7, Ms4a4b, Gzma"	T-natural killer	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Ventricular cardiomyocytes	"Corin, Fhl2, Ptgds, Trdn, Grm1, Mypn, Myocd, Ryr2, Ckmt2, Pde4d, Ldb3, Oxct1, Ivns1abp, Myom1, Cdh2, Pip5k1b, Sorbs1, Tnnt2, Esrrg, Acss1, Pde4b, Pcdh7, Ppargc1a, Shroom3, Fgf13, Asb11, Mlip, Alpk2, Tbc1d4, Fhod3, Fstl4, Pde4dip, Nexn, Rcan2, Cpeb3, Myh6"	Ventricular cardiomyocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Arterial cells	"Nrp1, Efnb2"	Arterial cells	Tissue	Heart	30075129	Cell Stem Cell	Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities	"GSE115618, GSE116718"
Mouse	Cardiomyocytes	"Nppa, Myl7, Sln"	Atrial cardiomyocytes	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Cardiomyocytes	"Pola1, Kif11, Lcorl, Atad5, Tmpo, E2f7, Top2a, Efcab11, Aoah, Cenpp, Depdc1b, Lcp1, Diaph3, Dab2, Atad2, Runx1, Cep192, Lmnb1, Nrp2, Prim2, Tnfrsf11a, Mrc1, Knl1, Tpx2, Ect2, Iqgap3, Adgrl2, Smc2, Cit, Ezh2, Mki67, Slc9a9, Myo1e, Kif23, Kif4, Brip1, Smc4"	Atrial cardiomyocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Cardiomyocytes	"Pam, Nppa, Myl4, Sln, Myl7"	Atrial cardiomyocytes	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Cardiac cells	"Nppa, Itga6"	Atrial cells	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Cardiac cells	"Cx30.2, Cx43, Cx40, Nppa, Myl2_"	Atrial-nodal transitional cells	Tissue	Heart	30765799	Sci Rep	Using Gjd3-CreEGFP Mouse to examine atrioventricular node morphology and composition	GSE118932
Mouse	Cardiac cells	"Calca, Mest, Myl2, Myl3, Crip1, Itga6, Etv1, Casq1, Nppb, Obscn, Smpx, Myh7, Ankrd1, Hopx, Nppa"	Atrium	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Dendritic cells	Cd209a	Dendritic cells	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Endothelial cells	"Cdh5, Pecam1"	Endothelial cells	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Fibroblasts	"Cola1, Pdgfra, Tcf21"	Fibroblasts	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Granulocytes	"Ccr1, Csf3r, S100a9"	Granulocytes	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Lymphocyte cells	"Ms4a1, Cd3e, Klrb1c, Ncr1"	Lymphocytes	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Muscle cells	"Acta2, Tagln"	Smooth muscle cells	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Fibroblasts	Col1a1	Fibroblasts	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Muscle cells	Myl9	Muscle cells	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Fibroblast-like cells	Dcn	Fibroblast-like cells	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Muscle-like cells	Acta2	Smooth muscle-like cells	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Pericytes	"Rgs5, Des"	Pericytes	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	B cells	"Cd79a, Cd79b, Ly6d, Mzb1"	B cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Dendritic cells	"Cd209a, Cd74, Flt3, H2-Eb1"	Dendritic cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Granulocytes	"S100A8, S100A9, Ngp, Camp"	Granulocytes	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Lymphocyte cells	"Cd3d, Nkg7, Cd8b1, Cd79a"	Lymphocytes	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Mast cells	"Calca, Furin, Il1rl1"	Mast cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Monocytes	"Ly6c2, Ccr2, Csf1r"	Monocytes	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Myeloid cells	"Adgre1, Itgax, Cd14, Csf1r, Lgals3, Ccr2, Cd68, Ly6c2, Cd209a"	Myeloid cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Natural killer (NK) cells	"Klrb1c, Ncr1, Klra8, Klrc1"	Natural killer (NK) cells	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Macrophages	"Adgre1, Cd14, Fcgr1, Csf1r"	Atherosclerosis-associated macrophages	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Macrophages	"Ccl3, Il1b, Il1a, Nlrp3, Cebpb, Egr1, Phldal, Nfkbiz, Nfkbid, Ier3, Zpf36, Nr4a1"	Inflammatory macrophages	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Macrophages	"F13a1, Lyve1, Ccl24, Ccl9, Folr2, Cbr2, Mrc1, Pf4, Txnip"	Res-like macrophages	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Macrophages	"Trem2, Cd9, Spp1, Hvcn1, Ctsd, Ctsb, Ctsz"	TREM2hi macrophages	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	B cells	"Itgam, Cd19, Spn, Ptprc, Kit, H2-Ab1"	B cells	Tissue	Heart	29545366	Circ Res	Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry	GSE21419
Mouse	Myeloid cells	"Itgam, Itgax, Ly6c1, Ly6g, Fcer1g, Adgre1"	Myeloid cells	Tissue	Heart	29545366	Circ Res	Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry	GSE21419
Mouse	T cells	"Cd5, Cd4, Cd8a, Cd8b1, Il2ra, Spn, Izumo1r"	T cells	Tissue	Heart	29545366	Circ Res	Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry	GSE21419
Mouse	Monocytes	"S100a8, S100a9, Cxcl2, Ccl2, Ccl3, F10, Tnf, Ly6c2"	Ly-6C+ inflammatory monocytes	Tissue	Heart	29545366	Circ Res	Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry	GSE21419
Mouse	Neural cells	"Ranbp1, Tuba1b, Sae1, Tubb5, Myl1, Aldh1b1, Birc5, H2afz, 2810417H13Rik, Cks2, Stmn1, Pttg1, Ube2c"	Neural cells c3	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Cardiac cells	"Cdk1, Ccnb1"	Cardiac reprogramming of Thy1-positive (Thy1+) cells	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Cardiac cells	Nkx2-5	Cardiac cells	Organoids	Heart	31320323	Development	Nkx2-5 defines a subpopulation of pacemaker cells and is essential for the physiological function of the sinoatrial node in Mouse	GSE130461
Mouse	Glial cells	"Gria3, Dlgap1, Map2, Abca8b, Klhl29, Aspa, Iqgap2, Gfra2, Matn2, Deptor, Il1rap, Ncam2, Afap1l2, Snca, Adam23, Frmd4a, Zeb2, Frmd5, Pappa, Epb41l4b, Chl1, Gpm6b, Tenm3, Il34, Cadm1, Scn7a, Kcnh8, Adgrl3, Slc22a23, Slc35f1, Adgrg6, Ncam1, Mbp, Egflam, Zfp5"	Cardiac glial cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Cardiac cells	"Abcg2, Alcam, Cd34, Eng, Gata4, Ly6a, Mef2c, Nkx2.5, Ptprc"	Cardiac progenitors	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	Cardiac cells	c-kit	Cardiac progenitors	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Cardiomyocytes	cTnT	Cardiomyocytes	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Cardiomyocytes	Tnni3	Cardiomyocytes	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Cardiomyocytes	Tnni3	Cardiomyocytes	Tissue	Heart	31142541	Development	Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development	GSE122403
Mouse	Cardiomyocytes	Tnnt2	Cardiomyocytes	Tissue	Heart	31216470	Cell Rep	Rational Reprogramming of Cellular States by Combinatorial Perturbation	GSE117795
Mouse	Cardiomyocytes	NA	Cardiomyocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	NA	Cardiomyocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	NA	Cardiomyocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	"1110034G24Rik, 1700020I14Rik, 2010111I01Rik, 4930402H24Rik, 4930512H18Rik, 9130011E15Rik, A930015D03Rik, Aak1, Abcd3, Abhd18, Ablim1, Abtb2, Acacb, Acadm, Acat1, Aco2, Acot13, Acsl1, Acss1, Actn2, Acyp2, Adamts6, Adamtsl5, Adk, Adprhl1, Adra1a, Agl, Agtr1a, AI314180, Akap6, Alpk2, Alpk"	Cardiomyocytes(A)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	"9530026P05Rik, Abhd18, Ablim2, Acss1, Actc1, Actn2, Adam19, Adamts6, Adgrl2, Adprhl1, Aff2, Agl, Akap6, Alpk2, Angpt1, Ank2, Ank3, Ankrd1, Ano4, Arfgef1, Arhgap21, Arhgap31, Art1, Art3, Asb14, Asb2, Atcayos, Atp1a1, Atp2a2, Auts2, Bmpr1a, Cacnb2, Camk1d, Camk2d, Cap2, Casq2, Casz1, Ccdc141, C"	Cardiomyocytes(C)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	"1700016D06Rik, 1700020I14Rik, 2010107E04Rik, 2410015M20Rik, Acaa2, Acadl, Acadm, Acadvl, Acat1, Aco2, Acot13, Acsl1, Actc1, Actn2, Adgrl4, Adprhl1, Aes, Ak1, Aldoa, Ankrd1, Aqp1, Art1, Art3, Asb2, Asph, Asxl2, Atp1a1, Atp1a2, Atp2a2, Atp5a1, Atp5b, Atp5c1, Atp5d, Atp5e, Atp5f1, Atp5g1, Atp5"	Cardiomyocytes(B)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Cardiomyocytes	"Spi1, Adgre1, Cd163, Cmah, Ikzf1, Dock2, Aoah, Ly86, Syk, Mctp1, Iqgap2, Rnf180, Lcp1, Epsti1, Dab2, Slc7a8, Mtss1, Fam49b, Cd86, Runx1, Myo1f, Pik3ap1, Ptprj, Pstpip2, Inpp5d, Tnfrsf11a, Ptprc, Dclre1c, Mrc1, Zeb2, Kcnip4, Tbxas1, Frmd4b, Ctsc, Slc9a9, Z"	Cardiomyocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Cardiomyocytes	Myh6	Cardiomyocytes	Tissue	Heart	32220304	Dev Cell	Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing	GSE130699
Mouse	Cardiomyocytes	"Myh6, Atp5b, Mdh2, Sod2, Mb"	CM4	Tissue	Heart	32220304	Dev Cell	Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing	GSE130699
Mouse	Cardiomyocytes	"Myh6, Ddc"	CM3	Tissue	Heart	32220304	Dev Cell	Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing	GSE130699
Mouse	Cardiomyocytes	"Myh6, Xirp2, Cd44, Ankrd1"	CM5	Tissue	Heart	32220304	Dev Cell	Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing	GSE130699
Mouse	Cardiomyocytes	"Myh6, Top2a, Lockd, Casc5"	CM2	Tissue	Heart	32220304	Dev Cell	Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing	GSE130699
Mouse	Cardiomyocytes	Actc1	Cardiomyocytes	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Progenitor cells	"Flk1, Gata6"	Cardiovascular progenitors	Organoids	Heart	33176168	Cell Stem Cell	Capturing Cardiogenesis in Gastruloids.	GSE158999
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	Tissue	Heart	30075129	Cell Stem Cell	Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities	"GSE115618, GSE116718"
Mouse	Hematopoietic stem cells	Sema3g	Hematopoietic stem cells	Tissue	Heart	30075129	Cell Stem Cell	Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities	"GSE115618, GSE116718"
Mouse	Endothelial cells	Cdh5	Endothelial cells	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	Fibroblasts	"Pdgfra, Col1a1"	Fibroblasts	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	Muscle cells	Acta2	Smooth muscle cells	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	T cells	Cd3e	T cells	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	Endothelial cells	"CD31, CD105, vimentin"	Endothelial cells	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Fibroblasts	"DDR2, CD90"	Fibroblasts	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Hematopoietic stem cells	"c-kit, Sca1"	Hematopoietic stem cells	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Muscle cells	NA	Smooth muscle cells	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Endothelial cells	Kdr	Endothelial cells	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Endothelial cells	Ccl21a	Lymphatic endothelial cells (LECs)	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Muscle cells	Tagln	Vascular smooth muscle cells	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Macrophages	"Ptprc, H2-Eb1, Cd86, Selplg, Cd14"	Macrophages	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	Ehd3	Aortic endothelial cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	"Adgre1, Fcgr1, C1qa"	Macrophages	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Endothelial cells	"Cdh5, Pecam1, Cav1, Fabp4"	Vascular endothelial cellss	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Fibroblasts	"Ddr2, Tcf21, Col3a1, Col1a2, Col1a1"	Fibroblasts	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Fibroblasts	"Dcn, Gsn"	Fibroblasts	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Immune cells	"C1qa, H2-Eb1"	Immune cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Immune cells	C1qa	Immune cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Mesenchymal cells	"vimentin4, Dcn, Col1a1, Ddr2, Col3a1, Eln, Fn1, Acta, Tagln5"	Smooth muscle cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Myofibroblasts	"Myh11, Tcf21"	Myofibroblasts	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Muscle cells	Myh11	Smooth muscle cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Fabp4, Cdh5, Cav1"	Vascular endothelial cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Cdh5, Pecam1, Fabp4, Cav1"	Vascular endothelial cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Progenitor cells	c-kit	Common myeloid progenitors	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Muscle cells	"Myh11, Acta2, Tagln"	Vascular smooth muscle cells	Tissue	Heart	30385745	Nat Commun	Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy Mouse vessels	"GSE79436, GSE117963"
Mouse	Muscle cells	"Myh11, Acta2, Tagln, Ly6a"	VSMC-lineage cells	Tissue	Heart	30385745	Nat Commun	Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy Mouse vessels	"GSE79436, GSE117963"
Mouse	Muscle cells	"Myh11, Acta2, Tagln, Pde1c, Hand2"	AA region	Tissue	Heart	30385745	Nat Commun	Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy Mouse vessels	"GSE79436, GSE117963"
Mouse	Muscle cells	"Myh11, Acta2, Tagln, Hoxa7"	DT region	Tissue	Heart	30385745	Nat Commun	Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy Mouse vessels	"GSE79436, GSE117963"
Mouse	B cells	Cd19	B cells	Tissue	Heart	30479344	Nat Commun	Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells	GSE118237
Mouse	Dendritic cells	Itgax	Dendritic cells	Tissue	Heart	30479344	Nat Commun	Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells	GSE118237
Mouse	T cells	"Lef1, Ms4a4b, Cd8a"	Cytotoxic T cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	B cells	"Cd79b, Cd79a, Ly6d, Ptprcap"	B cells	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Monocytes	"Ms4a7, Spp1"	Monocytes	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Stromal cells	"Sparc, Fabp4, Igfbp7, Crip2"	Stromal cells	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Myeloid cells	"Csf1r, Cd14, Adgre1, Cd68"	"Canonical myeloid cell, monocyte, and macrophages"	Cell line	Heart	30830865	JCI Insight	"Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression"	GSE123587
Mouse	Endocardial cells	Npr3	Endocardial cells	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Endocardial cells	"Npr3, Pecam1"	Endocardial cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endocardial cells	Npr3	Endocardial cells	Tissue	Heart	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endocardial cells	"Ecscr, Cdh5"	Endocardial cells	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Endocardial cells	"Efnb2, Vwf, Actn1, Plagl1, Nuak1, Pecam1, Nxn, Smoc1, Npr3, Rps6ka2, Crim1, Sncaip, Setbp1, Cemip2, Fgf14, Cfh, Ptpn14, Eng, Acvr1, Epha7, Unc13b, Eln, Plxna4, Foxp1, Tmtc1, Dennd5b, Bmx, Pir, Gpm6a, Pdlim3, Cdh11, Cgnl1, Thsd4, Kank1, Itgbl1, Kcnc2, Tmtc"	Endocardial cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Endocardial cells	"Tm4sf1, Cytl1, Tmem108, Vwf, Npr3"	Endocardial cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Endocrine cells	Irx5	Endocrine cells	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Endothelial cells	"Cdh5, Plvap, Emcn, Sox17, Pecam1, Gpr116"	Endothelial/Endocardial cell	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Endothelial cells	"Etv2, Tal1, Lmo2"	Hematoendothelial Progenitors	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Endothelial cells	"Hand2, Msx1, Tbx20, Gata4, Nfatc1, Smad6"	Endothelial-to-Mesenchymal Transition cells	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	B cells	"Cd79a, Ms4a1"	B cells	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Dendritic cells	"Cd209a, Itgam"	Dendritic cells	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Endothelial cells	"Kdr, Pecam1"	EC1 (Endothelial cells 1)	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Fibroblasts	"Col1a1, Pdgfra"	Fibroblasts	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Myeloid cells	"Cd68, Itgam, Ifitm6, Lrg1, Mcemp1, Sell, Gm9733"	M1 monocyte	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Natural killer (NK) cells	"Klrk1, Ccl5"	Natural killer (NK) cells	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Macrophages	"C1qb, C1qa, C1qc, Ms4a7"	M1 macrophage	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Macrophages	"Hpgds, Olfml3, Cd83"	M2 macrophage	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Epicardial cells	Rspo1	Epicardial cells	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Epicardial cells	Wt1	Epicardial cells	Tissue	Heart	31142541	Development	Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development	GSE122403
Mouse	Epicardial cells	Lhx9	Epicardial cells	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Epicardial cells	Wt1	Epicardial cells	Tissue	Heart	31216470	Cell Rep	Rational Reprogramming of Cellular States by Combinatorial Perturbation	GSE117795
Mouse	Epicardial cells	"Upk3b, Upk1b"	Epicardial cells	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Epicardial cells	"1700112E06Rik, 9030624G23Rik, 9530026P05Rik, Abcb1b, Abi1, Adamtsl1, Adgrd1, Adk, Aebp1, Agap1, Aldh1a2, Ano1, Ano6, Ap4e1, Aqp1, Arhgap18, Arhgap29, Arhgef12, Arid4b, B4galt1, Bcam, Bicc1, Bicd1, Bmpr1a, Bnc2, Bsg, C3, Cacnb2, Cadm2, Cald1, Calr, Ccdc171"	Epicardial cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	"Pecam1, Cldn5, Icam2, Esam, Tm4sf1, Egfl7"	Adventitial endothelial cells (ADV-ECs)	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	B cells	"Cd79a, Cd19, Ptprc"	B cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Dendritic cells	"Flt3, Zbtb36, Itgax"	Dendritic cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Erythrocytes	"Gypa, Snca"	Erythrocytes	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Fibroblasts	"Ddr2, Col1a1, Serpinh1"	Fibroblasts	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Lymphocyte cells	"Il1rl121, Gata3, Ptprc"	Innate lymphoid cells (ILCs)	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Myeloid cells	"Cd14, Cebpb, Ptprc"	Monocytes/macrophages	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Myeloid cells	"Cd14, Cebpb, Ptprc"	Monocytes/macrophages	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Myeloid cells	"Cd14, Cebpb, Ptprc"	Monocytes/macrophages	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Myeloid cells	"Cd14, Cebpb, Ptprc"	Monocytes/macrophages	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Natural killer (NK) cells	"Gzma, Gzmb, Klrb1c, Ptprc"	Natural killer (NK) cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Muscle cells	"Tagln, Flna, Myh11, Tpm2, Acta2"	Smooth muscle cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Stem cells	"Sca1, Cd34, Tbx18"	Stem cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	Epicardial cells	"1700112E06Rik, 9030624G23Rik, 9530026P05Rik, Abcb1b, Abi1, Adamtsl1, Adgrd1, Adk, Aebp1, Agap1, Aldh1a2, Ano1, Ano6, Ap4e1, Aqp1, Arhgap18, Arhgap29, Arhgef12, Arid4b, B4galt1, Bcam, Bicc1, Bicd1, Bmpr1a, Bnc2, Bsg, C3, Cacnb2, Cadm2, Cald1, Calr, Ccdc171"	Epicardial cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Epicardial cells	"Rarres2, Igfbp5, Muc16, Msln, Upk3b"	Epicardial cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Epicardial cells	"Wt1, Tbx1, Cebpb, Krt18"	Epicardial cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Glial cells	"Plp1, Kcna1"	Glial cells	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Heart	31142541	Development	Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development	GSE122403
Mouse	Mesenchymal cells	Fbln2	Mesenchymal cells	Tissue	Heart	31142541	Development	Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development	GSE122403
Mouse	Endothelial cells	"Gpihbp1, Pecam1, Ccl21a, Cytl1, Fabp4"	Endothelial cells	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Endothelial cells	"Gpihbp1, Pecam1, Ccl21a, Cytl1, Fabp4"	Endothelial cells	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Endothelial cells	"Gpihbp1, Pecam1, Ccl21a, Cytl1, Fabp4"	Endothelial cells	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Fibroblasts	"Serpinf1, Lum, Clec3b, Gsn, Dcn"	Fibroblasts	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Monocytes	"Pf4, C1qb, Retnla, C1qa, Lyz2"	Monocytes	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Muscle cells	"Myh11, Tpm2, Myl9, Tagln, Acta2"	Vascular smooth muscle cells	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Fibroblasts	Col1A1	Cardiac fibroblasts	Tissue	Heart	31216470	Cell Rep	Rational Reprogramming of Cellular States by Combinatorial Perturbation	GSE117795
Mouse	Fibroblasts	Col1a1	Ccardiac fibroblastss	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	Endothelial cells	"Pecam1, Cd31"	Endothelial cells	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	Muscle cells	Rerg	Smooth muscle cells	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	Hepatocytes	Onecut2	Hepatocytes	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Fibroblasts	"Lox, Ctgf"	Fibroblasts	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Myeloid cells	"Spp1, Lyz2"	Myeloid cells	Tissue	Heart	31271750	Cell Stem Cell	Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming	GSE131328
Mouse	Myofibroblasts	Acta2	Myofibroblasts	Tissue	Heart	31359001	Nat Med	Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.	GSE131778
Mouse	Mesenchymal cells	"Postn, Cthrc1"	Mesenchymal cells	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Muscle cells	"Rgs5, Cxcl12, Acta2, Tagln, Cnn1, Myl9"	Vascular smooth muscle cells	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Progenitor cells	Tw2	Interstitial myogenic progenitor	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Leukocytes	Lyz2	Leukocytes	Tissue	Heart	29449267	Cancer Res	Single-Cell Transcriptome Analyses Reveal Endothelial cells Heterogeneity in Tumors and Changes following Antiangiogenic Treatment.	GSE110501
Mouse	Endothelial cells	CD31	Endothelial cells	Tissue	Heart	31572976	Nat Metab	Endothelial TGF-beta signalling drives vascular inflammation and atherosclerosis.	GSE134557
Mouse	Macrophages	"PD-L2, CD301"	Alternatively activated M2 macrophages	Cell line	Heart	30830865	JCI Insight	"Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression"	GSE123587
Mouse	Macrophages	"Adgre1, Fcgr1"	Macrophages	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Macrophages	"Adgre1, Csf1r, Fcgr1, Cd68, F13a1, Lyve1, Gas6"	Macrophages	Tissue	Heart	29545365	Circ Res	Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis	GSE97310
Mouse	Macrophages	Mrc1	Macrophages	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Macrophages	"Ccl4, Cxcl2, Ccl3"	Inflammatory macrophages	Cell line	Heart	30830865	JCI Insight	"Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression"	GSE123587
Mouse	Macrophages	"Cd11b, Cd68, Adgre1"	Macrophages	Tissue	Heart	30479344	Nat Commun	Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells	GSE118237
Mouse	Macrophages	NA	Macrophages	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Macrophages	NA	Macrophages	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Macrophages	"Btg1, Ltb, Coro1a, Rac2, Cd52"	Macrophages	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Macrophages	Spi1	Macrophages	Tissue	Heart	31201182	Development	A cellular atlas of Pitx2- dependent cardiac development	GSE131181
Mouse	Macrophages	Lys6C	Macrophages	Tissue	Heart	31216470	Cell Rep	Rational Reprogramming of Cellular States by Combinatorial Perturbation	GSE117795
Mouse	Macrophages	"Ptprc, Cd45"	Macrophages	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	Macrophages	Lgals3	Macrophages	Tissue	Heart	31359001	Nat Med	Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.	GSE131778
Mouse	Macrophages	"Fcgr1, Adgre"	Macrophages	Tissue	Heart	31365875	Cell Rep	Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells.	NA
Mouse	Macrophages	Mac-2	Macrophages	Tissue	Heart	31572976	Nat Metab	Endothelial TGF-beta signalling drives vascular inflammation and atherosclerosis.	GSE134557
Mouse	Macrophages	"Adgre, Cd68"	Macrophages	Tissue	Heart	31594470	Circ Res	Context-specific regulation of surface and soluble IL7R expression by an autoimmune risk allele	NA
Mouse	Macrophages	"Adgre1, Cd68, Csf1r"	Macrophages	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Macrophages	"Cd68, Lgals3, Trem2"	Macrophages	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Adipocytes	"1700112E06Rik, 4732471J01Rik, 4930402H24Rik, 4930556N13Rik, 4931406C07Rik, 4933406I18Rik, Aacs, Abcd3, Acaca, Acacb, Acadl, Acly, Aco2, Acox1, Acsl1, Acss2, Acss3, Acvr1c, Adam12, Adamts12, Adipoq, Adipor2, Adra1a, Adrb3, Agmo, Agpat2, Ahcyl2, Akap1, Aldh"	Adipocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Adipocytes	"1700112E06Rik, 4732471J01Rik, 4930402H24Rik, 4930556N13Rik, 4931406C07Rik, 4933406I18Rik, Aacs, Abcd3, Acaca, Acacb, Acadl, Acly, Aco2, Acox1, Acsl1, Acss2, Acss3, Acvr1c, Adam12, Adamts12, Adipoq, Adipor2, Adra1a, Adrb3, Agmo, Agpat2, Ahcyl2, Akap1, Aldh"	Adipocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Macrophages	"Ccl8, Fbxo32"	Macrophage cluster 3	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"C1qa, Cd68"	Macrophages	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Endothelial cells	NA	Endothelial cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	NA	Endothelial cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	NA	Endothelial cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	"1700112E06Rik, 4931406P16Rik, 9330175M20Rik, 9530026P05Rik, A930011G23Rik, Acer2, Airn, Akt3, Aplp2, Apoe, App, Arhgap31, Arhgef3, Asxl2, Atp1b3, Bace2, Bgn, Bmp6, Bmpr2, Bmx, Bsg, Calm2, Cd200, Cd81, Cd9, Cdh11, Cfh, Cgnl1, Chrm3, Clic1, Col5a2, Cox6a1, Cpe, Cped1, Crim1, Crip1, Crip2, Csga"	Endothelial (A)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	"1810011O10Rik, 4921511C10Rik, 4930448N21Rik, 4931406P16Rik, 9330175M20Rik, Ablim1, Actb, Actg1, Adgrf5, Adgrl2, Adgrl4, Apbb2, App, Aqp1, Arhgap18, Arhgap31, Arhgef3, Arl15, Atxn1, B2m, Bsg, Calm1, Cav1, Ccdc85a, Cd200, Cd36, Cd81, Cd9, Cdh13, Cdh5, Col4a1, Col4a2, Cox6a1, Cox6c, Crip1, Cr"	Endothelial (B)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Endothelial cells	"1700025G04Rik, 4930448N21Rik, 4930578G10Rik, 4931406P16Rik, 9330175M20Rik, Abhd17b, Abi3bp, Adam10, Adamtsl1, Aplp2, App, Aqp1, Arap3, Arhgap29, Asap1, Atp11c, Calcrl, Ccl21a, Ccser1, Cd9, Chrm3, Cldn5, Cmip, Cp, Cped1, Cpne8, Crim1, Csgalnact1, Ctdspl, D5Ertd615e, Dab2, Dapk2, Dennd4a"	Endothelial (C)	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Macrophages	Gpr34	Macrophage cluster 4	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	Cd93	Macrophage cluster 5	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Fibroblasts	NA	Fibroblasts	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Granulocytes	"4933406I18Rik, Acaca, Acacb, Acsl1, Acss3, Acvr1c, Adipor2, Car3, Cdo1, Cfd, Chpt1, Cidec, Dbi, Ebf1, Efna5, Erbb4, Fabp4, Fam13a, Fry, G0s2, Ghr, Gm26917, Gphn, Ifi27, Immp2l, Lipe, Neat1, Negr1, Nfia, Nrg4, Pcx, Pde3b, Pik3r1, Plcb1, Plin1, Pnpla3, Ppar"	Granulocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Granulocytes	"4933406I18Rik, Acaca, Acacb, Acsl1, Acss3, Acvr1c, Adipor2, Car3, Cdo1, Cfd, Chpt1, Cidec, Dbi, Ebf1, Efna5, Erbb4, Fabp4, Fam13a, Fry, G0s2, Ghr, Gm26917, Gphn, Ifi27, Immp2l, Lipe, Neat1, Negr1, Nfia, Nrg4, Pcx, Pde3b, Pik3r1, Plcb1, Plin1, Pnpla3, Ppar"	Granulocytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Immune cells	NA	Immune cells	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Macrophages	"Vcan, Plac8, Ly6c2"	Macrophage cluster 6	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"Ccr7, Wnt11, Clec10a, Tnip3"	Macrophage cluster 7	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"Tnf, Il-10, Cd207, Vsig4"	Macrophage cluster 8	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"Adgre4, Treml4"	Macrophage cluster 9	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	Pmp22	Macrophages 1	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"Milr1, Cxcl9, Ly6i, Nos2, Arg1, Ass1"	Macrophages 2	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	Adgre1	Macrophages	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Macrophages	"Lyve1, Timd4, Retnla, Cd163, Folr2, Klf2"	Mature macrophages	Tissue	Heart	30538339	Nat Immunol	Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction	GSE119355
Mouse	Natural killer (NK) cells	"Klrg1, Klrb1c"	Natural killer (NK) cells	Tissue	Heart	31732166	Immunity	Tissue-specific macrophage responses to remote injury impact the outcome of subsequent local immune challenge	GSE104342
Mouse	Natural killer (NK) cells	"Klrg1, Klrb1c"	Natural killer (NK) cells	Tissue	Heart	31732166	Immunity	Tissue-specific macrophage responses to remote injury impact the outcome of subsequent local immune challenge	GSE104342
Mouse	Macrophages	"Spp1, Pf4, Lgals3, Ftl1, Ctsb, Ctsd, Acp5, C1qb, C1qa, Hmox1"	Macrophages	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Macrophages	"Itgam, Mrc1, Adgre1, Ptprc, Cd68"	Macrophages	Tissue	Heart	32674599	Circulation	Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.	GSE150644
Mouse	Macrophages	"Adgre1, Csf1r, Mafb, Fcgr1"	Macrophages	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Macrophages	"Adgre1, Csf1r, Mafb, Fcgr1"	Macrophages	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Macrophages	"Lyz2, Ccl4, C1qb, Cxcl2, Cd74"	Macrophages	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Macrophages	"Adgre1, Itgam"	Macrophages	Tissue	Heart	32917889	Nat Commun	Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation	GSE155569
Mouse	Macrophages	"Adgre1, Itgam"	Macrophages	Tissue	Heart	32917889	Nat Commun	Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation	GSE155569
Mouse	Macrophages	"Adgre1, Itgam"	Macrophages	Tissue	Heart	32917889	Nat Commun	Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation	GSE155569
Mouse	Macrophages	"Ly6c1, Lgals3"	Macrophages	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	Macrophages	CX3CR1	Stem-like macrophages	Cell line	Heart	30830865	JCI Insight	"Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression"	GSE123587
Mouse	T cells	"Cd3g, _l2r, _tprc_nd_l7r, CD45RO, CD127"	Memory T cells	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Progenitor cells	c-kit	Multipotent progenitors (mpps)	Organoids	Heart	30127033	Proc Natl Acad Sci U S A	Identification of a multipotent Twist2-expressing cell population in the adult heart	GSE118411
Mouse	Progenitor cells	"Isl1, Foxf1, Tbx1, Rgs5, Osr1, Fgf8"	Multipotent progenitors (mpps)	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Progenitor cells	"Rgs5, Irx3, Hand2, Fgf8, 3632451O06Rik, Irx5, Smyd1, Mef2c, Isl1"	Anterior second heart field	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Progenitor cells	"Six1, Ebf2, Ebf1.1, Lhx2, Tbx1, Tlx1"	Branchiomeric Muscle Progenitors	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Progenitor cells	"Wnt2, Foxf1, Osr1, Gata4, Tbx5, Aldh1a2"	Posterior second heart field	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	B cells	CD19	B cells	Tissue	Heart	31945014	JCI Insight	Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men	GSE142515
Mouse	Myoblasts	"Mrvi1, Map2, Cacnb4, Plxdc1, Myo1b, Lin7a, Cfap54, Pde8b, Ebf2, Sema5a, Tnfrsf21, Nrxn1, Slc12a2, Pdgfrb, Rgs5, Plxdc2, Zeb2, Trpc3, Serpini1, Gucy1b1, Tbc1d1, Cald1, Rerg, Abcc9, Ano1, Dlc1, Il34, Arhgef17, Gucy1a1, Cacna1a, Art3, Mdga2, Dgkb, Adgrl3, In"	Myoblasts	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Dendritic cells	"Cd209a, Flt3, Itgax"	Dendritic cells	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Granulocytes	"Csf3r, S100a9"	Granulocytes	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Monocytes	"Ccr2, Ly6c2, Itgam"	Monocytes	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Muscle cells	"Spp1, Acta2, Mgp"	Smooth muscle cells	Tissue	Heart	31988506	Nat Nanotechnol	Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis.	NA
Mouse	Adipocytes	"Pparg, Lrp3, Slc1a5, Prkar2b, Slc1a3, Por, Acsl1, Slc36a2, Acaca, Tshr, Smoc1, Adcy5, Csad, Pcsk5, Pcx, Gpam, Cyp2e1, Rgs7, Acvr1c, Pck1, Car3, Bnc2, Scp2, Gpat3, Adipor2, Cidec, Plin1, Pde3b, Car5b, Slc27a1, Nrg4, Cdo1, Dpyd, Art3, Hacd2, Acss3, Sik2, Fa"	Adipocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	B cells	"Clec2g, Bcl11a, Cacna1e, Arhgef18, Pax5, Slamf6, Cmah, Ikzf3, Ikzf1, Dock2, Ly86, Syk, St6gal1, Runx1, Satb1, Pik3ap1, Stk17b, Inpp5d, Tmem163, Ptprc, Ralgps2, Cr2, Kynu, Itga4, Kcnq5, Coro2a, Rhoh, Stap1, Foxp1, Fchsd2, Swap70, Btk, Pou2af1, Ccnd3, Arhga"	B cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Endothelial cells	"Spi1, Adgre1, Cd163, Cmah, Ikzf1, Dock2, Aoah, Ly86, Syk, Mctp1, Iqgap2, Rnf180, Lcp1, Epsti1, Dab2, Slc7a8, Mtss1, Fam49b, Cd86, Runx1, Myo1f, Pik3ap1, Ptprj, Pstpip2, Inpp5d, Tnfrsf11a, Ptprc, Dclre1c, Mrc1, Zeb2, Kcnip4, Tbxas1, Frmd4b, Ctsc, Pde3b, Sl"	Cardiomyocyte-like endothelial cellss	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Endothelial cells	"Corin, Fhl2, Rbfox1, Myl2, Jph2, Trdn, Grm1, Mypn, Myocd, Dpf3, Ryr2, Ckmt2, Pde4d, Ldb3, Ivns1abp, Myom1, Cdh2, Pip5k1b, Sorbs1, Tnnt2, Esrrg, Grb14, Itgb6, Pde4b, Pcdh7, Fgf13, Sorbs2, Mlip, Alpk2, Ppargc1b, Fhod3, Pde4dip, Nexn, Prdm16, Rcan2, Cpeb3, M"	Endothelial cells myo10 high	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Endothelial cells	"Hdac9, Rasa4, B4galnt2, Fli1, Slfn3, Sema6a, Kitl, Ptprb, Nav3, Pecam1, Prkch, Rasgrf2, Ptprg, Shank3, Lims2, Podxl, Mgat4a, Pkp4, Itga6, Zbtb46, Adgrl2, D5Ertd615e, Flt1, Slc6a6, Mcf2l, Vegfc, Kirrel3, Ccdc85a, Mgll, Fgd5, Kcnc2, Tmtc2, Meox2, Eepd1, Etl"	Endothelial cells myo10 low	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Fibroblasts	"Celf2, Axl, Bicc1, Eya2, Lama2, Dcn, Egfr, Gfpt2, Abca8b, Meg3, Vcan, Scara5, Ebf2, Sdc2, Enpp2, Fstl1, Adamts5, Fkbp5, Zeb1, Lvrn, Col5a2, Col3a1, Lamc1, Ddr2, Plxdc2, Fbn1, Dclk1, Col15a1, Bnc2, Htra3, Pdgfra, Foxp2, Pcsk6, Gpm6b, Tenm3, Gnao1, Bmper, R"	Endothelial-derived fibroblasts	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Fibroblasts	"Celf2, Fbln1, Bicc1, Eya2, Dcn, Igf1, Egfr, Meg3, Vcan, Scara5, Ebf2, Angpt1, Vit, Fkbp5, Papss2, Col5a2, Col3a1, Cfh, Gsn, Mmp16, Svep1, Cntfr, Bnc2, Htra3, Foxp2, Eln, Nox4, Aff2, Col4a6, Gpm6b, Slit2, Pdlim3, Gnao1, Bmper, Tbx20, Rora, Thsd7a, Itgbl1"	Epicardial-derived fibroblasts	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Monocytes	"Mrvi1, Map2, Cacnb4, Plxdc1, Myo1b, Lin7a, Cfap54, Pde8b, Sema5a, Tnfrsf21, Nrxn1, Slc12a2, Pdgfrb, Mark1, Frmd4a, Rgs5, Trpc3, Serpini1, Gucy1b1, Errfi1, Tbc1d1, Cald1, Rerg, Abcc9, Ano1, Dlc1, Il34, Arhgef17, Gucy1a1, Art3, Mdga2, Dgkb, Adgrl3, Inpp4b"	Monocytes	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Fibroblasts	"Gria3, Bicd1, Rbfox1, Wt1, Sulf1, Wwc1, Efemp1, Npas3, Pde10a, Crim1, C3, Myo5b, Col3a1, Il18r1, Gpr39, Adam33, Kcnq5, Bnc2, Dnajc6, Sema3c, Shroom3, Plxna4, Ano1, Gpm6a, Cdh11, Thsd4, Kank1, Ptpn13, Grip1, Pawr, Slc2a13, Cdon, Pkhd1l1, Arhgap18, Tbce, Wd"	Neural crest-derived fibroblasts	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Muscle cells	"Corin, Tbx5, Myocd, Rgs6, Dpf3, Ryr2, Cap2, Ldb3, Angpt1, Fgf12, Enah, Myom1, Pip5k1b, Fgf14, Rp1, Pam, Tmem163, Tnnt2, Esrrg, Kcnj3, Zfp385b, Acss1, Pde4b, Pcdh7, Ppargc1a, Shroom3, Mtus2, Anapc15, Dkk3, Mlip, Alpk2, Tbc1d4, Rxfp1, Ano4, Pdzrn3, Pdzrn4"	Smooth muscle cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Endothelial cells	"Tcf7, Il7r, Arhgef18, Cd247, Slamf6, Cmah, Ikzf3, Ikzf1, Peli1, Dock2, Itk, Pik3r5, Iqgap2, Emb, Sidt1, Runx1, Satb1, Myo1f, Ms4a6b, Dgka, Il18r1, Ptprc, Prkcq, Itga4, Rasgrp1, Lef1, Kcnq5, Coro2a, Rhoh, Foxp1, Pde3b, Ets1, Cd226, Ccnd3, Arhgap45, Ripor2"	Vascular endothelial cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Neural cells	"Dlx5, Dlx2, Twist1, Nr2f1, Barx1"	Neural crest cells	Tissue	Heart	31341279	Nature	Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects	NA
Mouse	Neural cells	"Msx1, Twist, Sox9"	Neural crest-derived cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Neural cells	"Vwa1, Prnp, Cnp, Gpm6b, Mbp"	Neuronal cells	Tissue	Heart	31146585	Circulation	Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial cells Populations	NA
Mouse	Neural cells	"Dtx3, Trpc3, Notch3, Abcc9, Pgdfrb, Rgs5, Steap4, Kcnj8"	Neuronal cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Neural cells	"Dlst, Hnrnpa2b1, Sod2, Ppp1cb, Lpl, Pitpna, Trdn, Nmbr, Hexb, Ldb3, Nisch, Ndufa5, Hsp90ab1, Clip4, Grm8, Gpam, Rabgef1, Phkg1, Pam, Zfp106, Car1, Nceh1, Fastk, Tsc22d4, Coq7, Rps3, Fgfr2, Tpm1, Zranb3, Cox6b1, Zc3h7a, Hrc, Nexn, Camk1d, Ttc41, Bri3, Yjef"	Neuronal cells (ano1 high)	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Neural cells	"Efnb2, Col18a1, St8sia6, B4galnt2, Utrn, Nuak1, Ptprb, Efr3b, Pecam1, Fbln5, Arhgef28, Rasgrf2, Spata13, Myo10, Arhgap31, Epas1, Map4k3, Lama3, Sncaip, Pcsk5, Apba1, Afap1l2, Eps8l2, Podxl, Eng, Stmn2, Mecom, Apbb2, Flt1, Eln, Slc6a6, Adipor2, Bmx, Vegfc"	Neuronal cells (ano1 low)	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	Neural cells	"Abi1, Arhgap18, Bicc1, Bicd1, C3, Cdh11, Cdon, Celf2, Col3a1, Crip1, Dpp4, Efemp1, Efna5, Flrt2, Gpc3, Gpm6a, Igfbp5, Igfbp6, Il1rapl1, Kcnd2, Mast4, Muc16, Pbx1, Pcdh15, Pkhd1l1, Plce1, Plxna4, Ptprd, Rarres2, Rbfox1, Sema3d, Slit3, Sox6, Sugct, Sulf1, S"	Neuronal like	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Neural cells	"Abi1, Arhgap18, Bicc1, Bicd1, C3, Cdh11, Cdon, Celf2, Col3a1, Crip1, Dpp4, Efemp1, Efna5, Flrt2, Gpc3, Gpm6a, Igfbp5, Igfbp6, Il1rapl1, Kcnd2, Mast4, Muc16, Pbx1, Pcdh15, Pkhd1l1, Plce1, Plxna4, Ptprd, Rarres2, Rbfox1, Sema3d, Slit3, Sox6, Sugct, Sulf1, S"	Neuronal like	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Neutrophils	"Oasl2, Ngp, S100a8, Il18bp, Prok2, S100a9"	Neutrophils	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Neutrophils	Ly6g	Neutrophils	Tissue	Heart	30479344	Nat Commun	Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells	GSE118237
Mouse	B cells	"Cd79a, H2-DMb2"	B cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Dendritic cells	"H2ab1, Cd74"	Dendritic cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Endothelial cells	"Fabp4, Pecam1"	Endothelial cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Fibroblasts	"Col1a1, Gsn, Dcn"	Fibroblasts 1	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Fibroblasts	"Wif1, Dkk3"	Fibroblasts 2	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Fibroblasts	"Mt2, Timp1"	Fibroblasts 3	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Granulocytes	"S100a8, S100a9"	Granulocytes	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Endothelial cells	"Lyve1, Cldn5"	Lymphatic endothelial cells (LECs)	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Monocytes	NA	Monocytes	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Monocytes	NA	Monocytes	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Myofibroblasts	"Myofb, Cthrc1, Acta2, Postn"	Myofibroblasts	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Neutrophils	"Oasl2, Il18bp, Cxcl3, Gbps"	"L1a neutrophils, proinflammatory neutrophils"	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Muscle cells	"Rgs5, Vtn, Kcnj8"	Smooth muscle cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	Neutrophils	S100a8	Neutrophils	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Neutrophils	"Ngp, Prok2, Mmp8"	"Ngp mmp8 neutrophils, profibrotic neutrophi"	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Neutrophils	"S100a8, S100a9, Clec4e, Il1b, G0s2, Retnlg, Ifitm1, Gm5483, Cxcl2, Ccrl2"	Neutrophils	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Pericytes	"P2ry14, Pdgfrb"	Pericytes	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Pericytes	Pdgfrb	Pericytes	Organoids	Heart	30104715	Sci Rep	In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells	GSE114284
Mouse	Pericytes	Trpc3	Pericytes	Tissue	Heart	30143541	Development	Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition	GSE117893
Mouse	Pericytes	"9530026P05Rik, Abcc9, Adap2, Adap2os, Adgrl3, Airn, Akap13, Ano1, Apbb2, Arhgap26, Arhgap42, Arhgap6, Art3, Aspn, Cacna2d1, Cacnb4, Cald1, Chn1, Cobll1, Col4a1, Cped1, Creb3l2, Daam1, Dgkb, Dlc1, Dock6, Dtx3, Ebf1, Ebf2, Eif4g3, Epb41l2, Eps8, Farp1, Ferm"	Pericytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Pericytes	"9530026P05Rik, Abcc9, Adap2, Adap2os, Adgrl3, Airn, Akap13, Ano1, Apbb2, Arhgap26, Arhgap42, Arhgap6, Art3, Aspn, Cacna2d1, Cacnb4, Cald1, Chn1, Cobll1, Col4a1, Cped1, Creb3l2, Daam1, Dgkb, Dlc1, Dock6, Dtx3, Ebf1, Ebf2, Eif4g3, Epb41l2, Eps8, Farp1, Ferm"	Pericytes	Tissue	Heart	31723062	JCI Insight	Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart	NA
Mouse	Adipocytes	"Scd1, Acaca, Ctd, Plin1, Car3"	Adipocytes	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	B cells	"Uba52, Rn45s, Spnb2, Sdpr"	B cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Endothelial cells	"Arthgap45, Cd52, Gimap3, Il7r, Ms4a4b"	Endothelial cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Muscle cells	"Myh11, Tagln, Acta2"	Soomth muscle cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Endothelial cells	"Flt4, Reln, Mmrn1, Ccl21a"	Vascular endothelial cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	Plasma cells	"Jchain, Eaf2, Ighj3"	Plasma cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Plasma cells	"Jchain, Sdc1"	Plasma cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Plasmacytoid dentritic cells	"Ccr9, Klk1"	Plasmacytoid dentritic cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Platelet	Pf4	Platelet	Tissue	Heart	31694925	Sci Transl Med	Platelet regulation of myeloid suppressor of cytokine signaling 3 accelerates atherosclerosis	NA
Mouse	B cells	Cd79a	B cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Dendritic cells	"Cst3, Sept3"	Cst3+Sept3+ dendritic cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Dendritic cells	Flt3	Dendritic cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Endothelial cells	"Cd34, Dcn"	Endothelial cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Dendritic cells	"Il12b, Cacnb3"	Il12b+Cacnb3+ dendritic cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	B cells	"Ms4a1, Cd19, Ighd"	Immature B cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Lymphocyte cells	"Gata3, Il5"	Innate lymphoid cells (ILCs)	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Natural killer (NK) cells	"Ncr1, Ifng, Gzma"	Natural killer (NK) cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Endothelial cells	"Klf2, Pecam1, Cdh5"	Endothelial cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Fibroblasts-like cells	"Tcf21, Fn1"	Fibroblasts-like cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Lymphocyte cells	Ctla2a	Lymphoid	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Myeloid cells	Fcer1g	Myeloid cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	B cells	"Ly6d, Mzb1, Siglech, Igkc, Klk1, Ighm, Iglc1, Plac8"	B cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Dendritic cells	"Plbd1, H2-Eb1, H2-Aa, H2-DMa, H2-DMb1, H2-Ab1, Cd74, Naaa, Cst3"	Dendritic cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Endothelial cells	"Pecam1, Ctla2a, Egfl7, Ramp2, Cdh5, Cldh5, Plvap, Fabp4, Igfbp3"	Endothelial cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Epithelial cells	"Lgals7, Msln, Upk3b, Igfbp6, Dmkn, Ptgis, C3"	Epithelial cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Fibroblasts	"Mfap5, Col8a1, Cthrc1, Fbln2"	Fibroblasts	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Muscle cells	"Myh11, Gm13889, Rgs5, Mustn1, Myl9, Tagln"	Smooth muscle cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	Red cells	Hemgn	Red blood cells	Tissue	Heart	31142541	Development	Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development	GSE122403
Mouse	Red cells	Hba-a1	Red blood cells	Tissue	Heart	32521264	Cell Rep	PRMT1-p53 Pathway Controls Epicardial EMT and Invasion	GSE144271
Mouse	Endothelial cells	"Egfl7, Claudin-5"	Endothelial cells	Tissue	Heart	32668254	Cell Rep	Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis	GSE136786
Mouse	Mesenchymal cells	"Snail1, Tgfb2"	Mesenchymal cells	Tissue	Heart	32668254	Cell Rep	Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis	GSE136786
Mouse	Mesenchymal cells	"Twist, Prrx2, Loxl"	Transitioning to mesenchymal cells	Tissue	Heart	32668254	Cell Rep	Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis	GSE136786
Mouse	T cells	"Cd4, Foxp3, Ctla4"	Regulatory T cells (Treg)	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	Endothelial cells	"Cdh5, Pecam1, Vwf, Nos3"	Endothelial cells	Tissue	Heart	32674599	Circulation	Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.	GSE150644
Mouse	Muscle cells	"Myh11, Acta2"	Smooth muscle cells	Tissue	Heart	32674599	Circulation	Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.	GSE150644
Mouse	B cells	"Cd19, Cd79a, Jchain"	B cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	B cells	"Cd19, Cd79a, Jchain"	B cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Dendritic cells	Flt3	Dendritic cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Dendritic cells	Flt3	Dendritic cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Dendritic cells	Flt3	Dendritic cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Dendritic cells	Flt3	Dendritic cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Endothelial cells	"Pecam1, Cdh5, Kdr, Tie1"	Endothelial cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Endothelial cells	"Pecam1, Cdh5, Kdr, Tie1"	Endothelial cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Stromal cells	"Lum, Dcn, Cd34, Pdgfra, Ly6a"	Mesenchymal stem_stromal cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Monocytes	"Cd14, Fcgr3"	Monocytes	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Natural killer (NK) cells	"Ncr1, Gzmb, Fasl, Klrb1c, Klra3, Fcer1g, Gzma"	Natural killer (NK) cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Endothelial cells	"Pecam1, Cldn5, Ctla2a, Nts, Ccl21a"	Endothelial cells	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Fibroblasts	"Hsd11b1, Dpep1, Cygb, Gdf10, Smoc2"	Fibroblasts 1	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Fibroblasts	"1500015O10Rik, Prg4, Comp, Wif1, Thbs1"	Fibroblasts 2	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Fibroblasts	"Ly6a, Clec3b, C3, Mfap5"	Ly6a fibroblasts	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	Muscle cells	"Acta2, Myl9, Myh11, Tpm2, Tagln"	Smooth muscle cells	Tissue	Heart	32698686	Arterioscler Thromb Vasc Biol	Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm	GSE153534
Mouse	B cells	"Ebf1, Cd79a, Cd79b"	B cells	Tissue	Heart	32724455	Theranostics	Specific ablation of CD4+ T-cells promotes heart regeneration in juvenile Mouse	NA
Mouse	Schwann cells	"Plp1, Cnp"	Schwann cells	Tissue	Heart	29346760	Cell Rep	Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart	NA
Mouse	Schwann cells	"Plp1, Kcna1"	Schwann cells	Tissue	Heart	32130914	Cell Rep	Dynamic Interstitial Cell Responseduring Myocardial Infarction PredictsResilience to Rupture in Genetically Diverse Mouse	E-MTAB-7895
Mouse	B cells	"Cd79b, Cd19, Ms4a1, Ighd"	B cells	Tissue	Heart	32917889	Nat Commun	Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation	GSE155569
Mouse	Natural killer (NK) cells	"Trbc2, Thy1, Cd3g, Cd3d, Nkg7"	T cells/Natural killer (NK) cells	Tissue	Heart	32917889	Nat Commun	Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation	GSE155569
Mouse	Endothelial cells	Vcam1	Endothelial cells	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	Fibroblasts	"Col1a1, Col3a1, Fn1, Fsp1, Tnc, Vim"	Fibroblasts	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	Muscle cells	"Myh11, Cnn1, Acta2"	Smooth muscle cells	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	Stem cells	Ly6a	Stem cells	Tissue	Heart	32962412	Circulation	Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human	NA
Mouse	T cells	"Sell, Il7r"	Memory T-cells	Tissue	Heart	29545366	Circ Res	Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry	GSE21419
Mouse	T cells	Cd3e	T cells	Tissue	Heart	30479344	Nat Commun	Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells	GSE118237
Mouse	T cells	"Cd3e, Cd3d, Lef1, Cd8a"	TC1-Cd8	Tissue	Heart	30912746	eLife	"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury."	E-MTAB-7376 and E-MTAB-7365.
Mouse	T cells	"Cd3d, Ptprc"	T cells	Tissue	Heart	30943771	Arterioscler Thromb Vasc Biol	Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mouse Defined by Single-Cell RNA Sequencing	NA
Mouse	T cells	Themis	T cells	Tissue	Heart	31231540	Cell Discov	Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling	GSE129175
Mouse	T cells	CD3	T cells	Tissue	Heart	31572976	Nat Metab	Endothelial TGF-beta signalling drives vascular inflammation and atherosclerosis.	GSE134557
Mouse	T cells	"Col18a1, Dlgap1, Mrvi1, Actn1, Map2, Cacnb4, Myh11, Ppp1r12a, Csrp2, Myocd, Klhl29, Cap2, Mylk, Adcy5, Enah, Myom1, Mark1, Ccdc3, Itga8, Kcnab1, Serpini1, Eln, Cald1, Nox4, Ano1, Aff2, Col4a6, Rbpms, Sorbs2, Thsd4, Rbpms2, Kank1, Mamdc2, Lpp, Gucy1a1, Act"	T cells	Tissue	Heart	32013057	Cells	Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity	E-MTAB-8751
Mouse	T cells	"H20Eb1, Ighm, H2-Aa, H2-Ab1"	T cells	Tissue	Heart	32384695	Cells	Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mouse	NA
Mouse	T cells	Cd3g	T cells	Organoids	Heart	32431172	Circulation	Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis	GSE142564
Mouse	T cells	"Cd3g, Cd3d, Nkg7, Ms4a4b, Trbc2, Trbc1, AW112010, Ccl5, Gzma, Hmgb2"	T cells	Tissue	Heart	32621799	Cell	Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury	GSE152122
Mouse	T cells	"Cd3e, Cd8a, Lat, Trbc1, Ctla4, Gzmb"	T cells	Tissue	Heart	32674599	Circulation	Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.	GSE150644
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	T cells	"Cd3g, Cd4, Cd8b1"	T cells	Tissue	Heart	32689904	Circ Res	Impact of Local Allo-Immunity and Recipient Cells in Transplant Arteriosclerosis	"GSE149452, GSE140812 and GSE140968"
Mouse	Endothelial cells	"kdr, cdh5, cd34"	Endothelial cells	Organoids	Heart	33176168	Cell Stem Cell	Capturing Cardiogenesis in Gastruloids.	GSE158999
Mouse	Neural cells	"MAP2, TUJ1"	Classical neuronal cells	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"RBFOX3, SYN1"	Classical panneuronal cells	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Dentate granule cells (dgc)	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Dentate granule cells (dgc)	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Developing inhibitory neuron	NKX2.1	Developing inhibitory neuron	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Dorsal telencephalic	PAX6	Dorsal telencephalic	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Forebrain	FOXG1	Forebrain	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neuronal cells	GABA	Neuronal cells	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Mossy cells (mc)	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Mossy cells (mc)	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Astrocytes	Slc1a3	Astrocytes	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Neural cells	Grad1	Interneurons	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Neural cells	"Thy1, Mdh1"	Neurons	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Oligodendrocytes	Plp1	Oligodendrocytes	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Neural cells	Gria1	Pyramidal neurons	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Neural cells	"Gad1, Slc32a1, Sst, Grm1, Npy, Ngf"	Hippocamposeptal neurons	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99888
Mouse	Neural cells	"Gad1, Slc32a2, Sst, Grm1, Pnoc, Reln, Npy"	O-LM cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99889
Mouse	Neural cells	"Gad1, Slc32a3, Tac1, Satb1, Erbb4, Grm1, Pvalb, Sst_"	Basket cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99890
Mouse	Neural cells	"Gad1, Slc32a4, Tac1, Satb1, Erbb4, Grm1, Pvalb, Sst, Npy"	Bistratified cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99891
Mouse	Neural cells	"Gad1, Slc32a5, Tac1, Satb1, Erbb4, Grm1, Pvalb"	Oriens-Bistratified (O-Bi) cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99892
Mouse	Neural cells	"Gad1, Slc32a6, Pvalb, Satb1, Tac1, Snca, Pthlh, C1ql1"	Axo-axonic cells in isocortex	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99893
Mouse	Neural cells	"Gad1, Slc32a7, Cacna2d1, Lhx6, Nos, Reln"	MGE-derived neurogliaform cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99894
Mouse	Neural cells	"Gad1, Slc32a8, Cacna2d1, Lhx6, Nos, Reln_, Vwa5a"	Ivy cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99895
Mouse	Neural cells	"Gad1, Slc32a9, Cacna2d1, Lhx6, Nos1, Ndnf"	Caudal ganglionic eminence (CGE)-derived neurogliaform cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99896
Mouse	Neural cells	"Gad1, Slc32a10, Ntng1, Chrm2, Sst, Pvalb"	Trilaminar cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99897
Mouse	Neural cells	"Gad1, Slc32a11, Ntng1"	Putative radiatum-retrohippocampal neurons that project to the retrosplenial cortex.	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99898
Mouse	Neural cells	"Gad1, Slc32a12, Cck, Cnr1, Sncg, Trp53i11, Cxcl14, Slc17a8"	Soma-targeting basket cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99899
Mouse	Neural cells	"Gad1, Slc32a13, Cck, Cnr1, Sncg, Trp53i11, Cxcl14, Calb1, Reln"	Dendrite-targeting cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99900
Mouse	Neural cells	"Gad1, Slc32a14, Cck, Cnr1, Sncg, Trp53i11, Calb1, Vip, Slc17a8, Sema5a, Calca"	Cck cells of other layers	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99901
Mouse	Neural cells	"Gad1, Slc32a15, Calb2, Vip_, Penk"	IS-1 cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99902
Mouse	Neural cells	"Gad1, Slc32a16, Calb2, Vip, Penk"	IS-2 cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99903
Mouse	Neural cells	"Gad1, Slc32a17, Calb2, Vip, Penk"	IS-3 cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99904
Mouse	Neural cells	"Gad1, Slc32a18, Sst, Nos1"	Both backprojection cells and PENK-positive projection cells	Tissue	Hippocampus	29912866	PLoS Biol	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics	GSE99905
Mouse	Glial cells	Cd9	Glial cells	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Astrocytes	"Slc1a3, Gfap, Aldoc, Glul"	Astrocytes	Tissue	Hippocampus	32341542	Nat Neurosci	Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network	GSE143758
Mouse	Astrocytes	"GFAP, APOE, AQP4, SLC1A2"	Astrocytes	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"TBR1, vGlut1"	Excitatory neurons	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"NEUROD6, SLC17A7"	Excitatory neurons	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"DLX1, GAD1"	Inhibitory neurons	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"RBFOX3, SYN1, SYT1, NRXN3, SNAP25"	Neurons	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	TBR1	Cortical neuron	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	vGlut1	Excitatory neuron	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	"FEZF2, BCL11B, CTIP2"	Deeper-layer cortical	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	SATB2	Upper-layer marker	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Neural cells	PROX1	Hippocampal granule cell	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Oligodendrocytes	"PLP1, MBP"	Oligodendrocytes	Tissue	Hippocampus	32726626	Cell Rep	In Vivo Chimeric Alzheimer Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons	GSE152867
Mouse	Astrocytes	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Astrocytes	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Neural cells	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Excitatory neurons	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Neural cells	"Gad1, Gad2, Kcnip1, Erbb4, Rbms3, Kcnmb2"	Inhibitory neurons	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Oligodendrocytes	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Oligodendrocyte precursors	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Oligodendrocytes	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Oligodendrocytes	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Neural cells	"Slc17a7, Nrn1, Nrgn, Fh12, Neurod2"	Pyramidal neurons	Tissue	Hippocampus	33084572	eLife	"Developmental, cellular, and behavioral phenotypes in a Mouse model of congenital hypoplasia of the dentate gyrus"	GSE157983.
Mouse	Neural cells	"Slc17a7, Fibcd1, Pex5l"	Dorsal CA1 excitatory Neurons	Tissue	Hippocampus	33299180	Nature	RUNX1 and CBFbeta-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development	GSE158843
Mouse	Vascular cells	Itm2a	Vascular cells	Tissue	Hippocampus	29724792	Genome Res	bigSCale:an analytical framework for big-scale single-cell data.	GSE60361
Mouse	Embryonic hypothalamus cells	"Gap43, Cldn5, S100a1, Zbtb20, Rgs5, Hba-a1, Ndufa4l2, Fabp7, Ptprz1, Plac8, Igfbp7, Malat1"	Embryonic hypothalamus cells	Tissue	Hypothalamus	31469823	PLoS Computational Biology	An iterative clustering method for single-cell RNA sequencing data	GSE45719
Mouse	Oligodendrocytes	Olig2	Oligodendrocytes	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Tanycytes	Rax	Tanycytes	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Tanycytes	Rax	Tanycytes	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Ependymal cells	Foxj1	Ependymal cells	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Ependymal cells	Foxj1	Ependymal cells	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Astrocytes	Ntsr2	Astrocytes	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Microglia cells	Cx3cr1	Microglia cells	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Oligodendrocytes	Olig2	Oligodendrocytes	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Neural cells	Esr1	Glutamatergic neurons	Tissue	Hypothalamus	31626771	Cell	Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior	NA
Mouse	Neural cells	Esr1	Glutamatergic neurons	Tissue	Hypothalamus	31626771	Cell	Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior	NA
Mouse	Neural cells	Esr1	Glutamatergic neurons	Tissue	Hypothalamus	31626771	Cell	Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior	NA
Mouse	Hematopoietic stem cells	NA	Hematopoietic stem cells	Tissue	Hypothalamus	31628891	J Thromb Haemost	Role of thrombomodulin expression on hematopoietic stem cells	pending
Mouse	Neural cells	Stmn3	Neuronal cells	Tissue	Hypothalamus	30941008	Front Neurosci	Tanycyte-Independent Control of Hypothalamic Leptin Signaling	GSE93374
Mouse	Astrocytes	Gfap	Astrocytes	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Neural cells	Slc321	Gabaergic neurons	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Neural cells	Slc17a6	Glutamatergic neurons	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Astrocytes	"Agt, Rgcc"	Mature astrocytes	Tissue	Hypothalamus	32868762	Nat Commun	The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development	GSE132355
Mouse	Lymphocyte cells	"Il1rl1, Gata3, Klrg1, Il4, Il5, Il13, Areg"	Innate lymphoid cells (ILCs)	Tissue	Ileum	32814028	Immunity	Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine.	GSE151152
Mouse	Paneth cells	Mmp7	Paneth cells	Tissue	Ileum	32814028	Immunity	Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine.	GSE151152
Mouse	Megakaryocytes	"Plek, Pf4, Gp9, Cd41a"	Megakaryocytes	Cell line	Ilscs	32492433	Cell Rep	Endocrine-Exocrine Signaling Drives Obesity-Associated Pancreatic Ductal Adenocarcinoma.	GSE124992
Mouse	Stem cells	"Runx2, Gli1"	Runx2+/Gli1+ niche cells	Tissue	Incisor	32783935	Cell Rep	Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling	NA
Mouse	Amplifying cells	Ki67	Transit-amplifying cells	Tissue	Incisor	32783935	Cell Rep	Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling	NA
Mouse	Hair cells	Pou4f3	Hair cells	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Epithelial cells	EpCAM	Epithelial cells	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Mesenchymal cells	"CD326-, CD49f-, CD34-"	Mesenchymal cells	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Neural cells	CD49f	Neurons	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Neural cells	CD49f	"Neurons, vascular endothelium and the sensory epithelial cells"	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Endothelial cells	CD34	Vascular endothelial cells	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Endothelial cells	"CD34, CD49f"	Vascular endothelial cells	Tissue	Inner cell	32579737	Laryngoscope	Cell Type-Specific Expression Analysis of the Inner Ear A Technical Report	NA
Mouse	Intestinal stem cells	"Lgr5, Olfm4"	Intestinal stem cells	Tissue	Intestine	29950724	Nature	Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche	NA
Mouse	Intestinal stem cells	Lgr5	Intestinal stem cells	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Intestinal stem cells	R26Ryfp	Intestinal stem cells	Tissue	Intestine	32027840	Mol Cell	Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters	GSE128671
Mouse	Intestinal stem cells	R26Ryfp	Intestinal stem cells	Tissue	Intestine	32027840	Mol Cell	Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters	GSE128671
Mouse	Intestinal stem cells	Cdca7	Intestinal stem cells	Tissue	Intestine	32084390	Cell Stem Cell	Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells	GSE130822
Mouse	Intestinal stem cells	Msi1	Intestinal stem cells	Tissue	Intestine	32726617	Cell Rep	Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.	GSE145866
Mouse	Intestinal stem cells	"Gkn3, Ascl2, Olfm4, Jun, Pdgfa, 2210407c18Rik"	Intestinal stem cells	Tissue	Intestine	32726617	Cell Rep	Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.	GSE145866
Mouse	Intestinal stem cells	"Igfbp, Ascl2"	Intestinal stem cells	Tissue	Intestine	32726617	Cell Rep	Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.	GSE145866
Mouse	Lo-1 cells	"Cd81, Grem1"	Lo-1 cells	Tissue	Intestine	32084389	Cell Stem Cell	Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient	GSE130681
Mouse	Lo-2 cells	Sfrp1	Lo-2 cells	Tissue	Intestine	32084389	Cell Stem Cell	Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient	GSE130681
Mouse	Monocytes	"Ly6c2, Ccr2, Hp, Emilin2"	Monocyte-derived cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Mural cells	"Vtn, Ptp4a3"	Mural cells	Tissue	Intestine	32796823	Nat Commun	Distinct fibroblast subsets regulate lacteal integrity through YAP/TAZ-induced VEGF-C in intestinal villi	GSE124488
Mouse	NA	"Ngb, Gsg1l, Col25a1"	Cluster 1	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Vwa5b1, Sv2b, Oprd1"	Cluster 2	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Penk, Sncb, Olfm3"	Cluster 3	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Cemip, Kcnip1"	Cluster 4	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Num, Pcdh10, Cbln2"	Cluster 5	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Skap1, Nefl, Nxph2"	Cluster 6	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Cdh9, Mgat4c, Klhl1"	Cluster 7	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	NA	Cluster 8	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Sst, Galnt5, Pantr1"	Cluster 9	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Trhde, Bean1, Neurod6"	Cluster 10	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Myrf, Nkain4, Cldn15"	Cluster 11	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Col11a1, Tmprss5, Car12"	Cluster 12	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Pigr, Klf5, Cdh1"	Cluster 13	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	NA	"Klhl4, Arap3, Radil"	Cluster 14	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	Paneth - distal	"Defa20, Defa32, Gm15308, Defa22, Defa21, Nupr1"	Paneth - distal	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Paneth - proximal	"Defa23, Clps, Defa17, Rnase1, Defa-rs1"	Paneth - proximal	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Proliferating cells	"Cdk4, Mcm5, Mcm6, Mki67, Pcna"	Proliferating cells	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Stem cells	"Slc12a2, Olfm4"	Proliferating or stem cells	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Regenerating cells	"Ascl2, Cdca7, Smoc2"	Regenerating uppe rcells	Tissue	Intestine	32084390	Cell Stem Cell	Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells	GSE130822
Mouse	Stem cell	"Stmn1, Hells, Tuba1b, Rrm2"	Singly profiled stem cell	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Stem cell	"Clu, Anxa1, Basp1, Cxadr"	Singly profiled stem cell	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Surface cells	"Cd68, Iba1, Cd11b, Ptprc"	Surface cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Ta	"Hmgb2, Ube2c, Top2a, Birc5, Mki67"	TA	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Ta cells	CDKN2A	Ta cells	Tissue	Intestine	32027840	Mol Cell	Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters	GSE128671
Mouse	Ta cells	CDKN2A	Ta cells	Tissue	Intestine	32027840	Mol Cell	Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters	GSE128671
Mouse	Telocytes	"Pdgfra, Bmp5, Bmp7, Bmp3"	Telocytes	Tissue	Intestine	32084389	Cell Stem Cell	Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient	GSE130681
Mouse	Trans colo	"Bmi1, Clu"	Trans colo	Tissue	Intestine	32084390	Cell Stem Cell	Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells	GSE130822
Mouse	Tuft cells	"Lrmp, Alox5ap, Dclk1, Ltc4s, Cd24a"	Tuft cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Stromal cells	"Mycn, Cd24a, Fez1, Gja1, Hm2a, Kif21a, Ly6h, Psip1, Slc22a17, Sox11, Tubb2b"	Atypical teratoid/rhabdoid tumors-SHH cell	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Stromal cells	"Anxa2, Arid5b, Bmp4, Ccdc80, Dcn, Hmox1, Ly6d, Ogn, Sfn, Tfpi"	Atypical teratoid/rhabdoid tumors-MYC cell	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Neural cells	"Bmi1, mTert, Hopx"	Neural cells c4	Tissue	Intestine	32726617	Cell Rep	Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.	GSE145866
Mouse	Crypt cells	Ly6a	Crypt cells	Tissue	Intestine	29950724	Nature	Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche	NA
Mouse	Goblet cells	MUC2	Goblet cells	Tissue	Intestine	29950724	Nature	Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche	NA
Mouse	Paneth cells	MMP7	Paneth cells	Tissue	Intestine	29950724	Nature	Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche	NA
Mouse	Colonocytes	"Fabp2, Car1"	Colonocytes	Tissue	Intestine	32084390	Cell Stem Cell	Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells	GSE130822
Mouse	Columnar cells	"Lgr5, Axin2, Ascl2"	Crypt-base columnar cells	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Enterocytes	Mttp	Enterocyte immature	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	"Agr2, Retnlb"	Enterocyte immature proximal	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	"Vil1, Myo1a"	Enterocyte mature	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	Mttp	Enterocyte mature	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	"Fabp6, Tmigd1"	Enterocyte mature distal	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	"Apoa4, Fabp2"	Enterocyte mature proximal	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Enterocytes	Apoc3	Enterocytes	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Enteroendocrine cells	Sst	Enteroendocrine cells	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Goblet cells	Muc2	Goblet cells	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Paneth cells	Lyz1	Paneth cells	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Stem cells	Olfm4	Stem cells	Organoids	Intestine	31019299	Nature	Self-organization and symmetry breaking in intestinal organoid development	GSE115956
Mouse	Epithelial cells	"Epcam, Vil1, Krt20, Cldn7, Cdh1"	Epithelial cells	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Lymphocyte cells	"Cd3e, Cd3g"	Lymphocyte cells	Organoids	Intestine	31019301	Nature	Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell	GSE123516
Mouse	Enterocytes	"Reg3b, Apoa1, Fabp6, Reg3g, Mep1b"	Enterocyte cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Enteroendocrine cells	"Chgb, Cck, Sct, Gip, Neurod1"	Enteroendocrine cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Goblet cells	NA	Goblet cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Goblet cells	NA	Goblet cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Goblet cells	NA	Goblet cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Stem cells	"Clca4, Amica1, Pdgfa, Kcne3, Hes1"	Stem cells	Tissue	Intestine	31442404	Cell	Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet	GSE112205
Mouse	Macrophages	"Ms4a7, Tgfbi, Cd74, H2-Aa, Cd68"	Macrophages	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Epithelial cells	"Epcam, Cldn4, Spint2"	Epithelial cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Immune cells	"Lyz2, Ms4a7, Apoe"	Immune cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Mesenchymal cells	"Cd44, Twist1, Vim, Anxa2, Col1a2"	Mesenchymal cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Microglia cells	"P2ry12, Siglech, Gpr34, Fcrls, TMEM119, CD33, GPR34, TREM2, CSF1R, MEF2C, SALL1, SALL3, CD68"	Microglia cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Myeloid cells	Cd68	Monocytes/macrophages	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Stem cells	"Slc12a2, Tubb5"	Stem cells	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Tuft cells	Rac2	Tuft cells	Tissue	Intestine	31900405	Mucosal Immunol	Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis	GSE131630
Mouse	Goblet cells	"Tff3, Muc2"	Goblet cells	Tissue	Intestine	32084390	Cell Stem Cell	Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells	GSE130822
Mouse	Dendritic cells	"Emb, Mcm6, Ccne1"	SP LysoDCs in G1/S	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Dendritic cells	"Emb, Cenpa, Ccnb2"	SP LysoDCs in G2/M	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Dendritic cells	Emb	SP LysoDCs	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Dendritic cells	"Emb, F11r"	DP LysoDCs	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Dendritic cells	"Emb, F11r, Cd24a, Plet1, Clec4d"	TP LysoDCs	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Dendritic cells	Tspan10	TN LysoDCs	Cell line	Intestine	32268097	Cell Rep	"Differentiation Paths of Peyer Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming"	GSE141776
Mouse	Pericytes	"Rgs5, Pdgfrb"	Pericytes	Tissue	Intestine	31470007	Gastroenterology	Interleukin 1 beta and Matrix Metallopeptidase 3 Contribute to Development of EGFR-dependent Serrated Polyps in Mouse Cecum	NA
Mouse	Paneth cells	"Lyz1, Defa17, Gm15284"	Paneth cells	Tissue	Intestine	32726617	Cell Rep	Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.	GSE145866
Mouse	Muscle cells	"Cnn1, Actg2"	Smooth muscle cells	Tissue	Intestine	32796823	Nat Commun	Distinct fibroblast subsets regulate lacteal integrity through YAP/TAZ-induced VEGF-C in intestinal villi	GSE124488
Mouse	T cells	Cd3g	T cells	Tissue	Intestine	31848709	Acta Neuropathol	Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance	GSE141534
Mouse	Neural cells	"Elavl4, Snap25, Oprk1, Brinp2, Tmem132c"	Cluster 0	Tissue	Intestine	33010250	Gastroenterology	Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.	GSE153202
Mouse	Enterocytes	"Alpi, Apoa1, Fabp1, Apoa4"	Enterocytes	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Enteroendocrine cells	"Chga, Chgb, Tac1, Tph1, Neurog3"	Enteroendocrine cells	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Goblet cells	"Muc2, Clca3, Tff3, Agr2"	Goblet cells	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Paneth cells	"Lyz1, Defa17, Defa22, Defa24, Ang4"	Paneth cells	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Stem cells	"Lgr5, Ascl2, Slc12a2, Axin2, Olfm4, Gkn3"	Stem cells	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Tuft cells	"Dclk1, Trpm5, Gfi1b, Il25"	Tuft cells	Organoids	Intestine	33029001	Nature	Phenotypic landscape of intestinal organoid regeneration	GSE147136
Mouse	Exocrine cells	Sox9	Duct cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Exocrine cells	Cpa1	Acinar cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Alpha cells	"Gcg, Arx, Cryba2, Mki67, Pcna, Mcm2"	SC-alpha cells	Tissue	Islets	32846125	Cell Rep	Single-Cell Transcriptome Profiling Reveals beta Cell Maturation in Stem Cell-Derived Islets after Transplantation	"GSE151117, GSE139535, GSE114297"
Mouse	Pancreatic cell	"Hhex, Rbp4"	Pancreatic delta cells	Tissue	Islets	32220307	Cell Metab	Beta Cell Dedifferentiation Induced by IRE1alpha Deletion Prevents Type 1 Diabetes	GSE144471
Mouse	Pracreatic beta cells	"MafA, Ucn3, Glut2, Ins1, Ins2"	Pracreatic beta cells	Tissue	Islets	32182217	J Clin Invest	Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-beta signaling	GSE137785
Mouse	Beta cells	"Ins1, Ins2"	Beta cells	Tissue	Islets	30799288	Cell Metab	Targeted Elimination of Senescent Beta Cells Prevents Type 1 Diabetes	GSE117770
Mouse	Beta cells	"MafA, Ucn3, Slc2a2"	Beta cell maturity	Tissue	Islets	32220307	Cell Metab	Beta Cell Dedifferentiation Induced by IRE1alpha Deletion Prevents Type 1 Diabetes	GSE144471
Mouse	Endocrine cells	Ins2	Beta cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Endocrine cells	Gcg	Alpha cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Endocrine cells	Sst	Delta cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Endocrine cells	Ppy	PP cell	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Endocrine cells	Ngn3	Endocrine progenitors	Tissue	Islets	32182217	J Clin Invest	Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-beta signaling	GSE137785
Mouse	Islet cells	"Irx2, Ttr"	Islet alpha cells	Tissue	Islets	32220307	Cell Metab	Beta Cell Dedifferentiation Induced by IRE1alpha Deletion Prevents Type 1 Diabetes	GSE144471
Mouse	Macrophages	"Cd68, Cd74"	Macrophages	Tissue	Islets	32304665	Cell	Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses	GSE137236
Mouse	Epithelial cells	"EpCAM, Krt8, Cldn10"	Epithelial cells	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	Mesenchymal cells	"Mmp2, Col1a1, Vim"	Mesenchymal cells	Tissue	Islets	32200801	Cell	Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr + Progenitors	OEP000249
Mouse	T cells	CD3	T cells	Tissue	Islets	32220307	Cell Metab	Beta Cell Dedifferentiation Induced by IRE1alpha Deletion Prevents Type 1 Diabetes	GSE144471
Mouse	Bowman capsule	Osr2	Bowman capsule	Tissue	Kidney	33420268	Sci Rep	Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney	GSE108291
Mouse	C.d.principal	"Frmpd4, Phactr1, Bmpr1b, Kif26b, Egfem1"	C.d.principal	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Cdica	"Aqp6, Slc4a9"	Cdica	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Cdicb	"Slc4a9, Slc26a4"	Cdicb	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Cdpc	"Aqp2, Fxyd4"	Cdpc	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	D.c.tubule	"Slc12a3, Trom6, Klhl3, Wnk1, Slc8a1"	D.c.tubule	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Dct1-2	"Slc12a3, Wnk1"	Dct1-2	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Distal tubule	"Umod, Slc12a3"	Convoluted tubule	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Distal tubule cells	"Kcne1, Scnn1a, Aqp2"	Collecting duct principal cells	Tissue	Kidney	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Distal tubule cells	Slc12a1	Distal tubule cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Distal tubule cells	Slc12a1	Distal tubule cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Distal tubule cells	"Slc12a1, Slc12a3, Calb1"	Distal tubule cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129800
Mouse	Distal tubule cells	"Calb1, Slc12a3"	Convoluted tubule cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Distal tubule cells	Ncc	Convoluted tubule cells	Tissue	Kidney	33159963	Kidney Int	Targeting fibroblast growth factor 23-responsive pathways uncovers controlling genes in kidney mineral metabolism.	GSE142113
Mouse	Ecting duct principal cell	"Aqp2, Hsd11b2, Rhbg"	Ecting duct principal cell	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Glomerular podocytes	Nphs1	Glomerular podocytes	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Inflammation	"Jak1, Stat3, I16ra"	Inflammation	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Intercalated cells	Atp6v1g3	Intercalated cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129802
Mouse	Intercalated cells	Atp6v1g3	Intercalated cells	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Jga	"Ren1, Slit3"	Jga	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	L.henle	"Scl12a1, Erbb4, Sgcz, Ptger3, Egf"	L.henle	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Loh collecting duct stalks	Aqp2	Loh collecting duct stalks	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Loh distal tubules	Slc12a3	Loh distal tubules	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Limb cells	"Umod, Slc12a1"	Loh thick ascending limb	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Limb cells	"Aqp1, Slc39a8"	Loh thin descending limb	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Loh ureteric bud tips	Ret	Loh ureteric bud tips	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Loop of henle	"Slc12a1, Umod"	Ascending loop of henle	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Loop of henle	"Cryab, Abg1"	Loop of henle	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Loop of henle	"Umpd, Egf, Slc13a1"	Loop of henle	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Mesangial cells	"Des, Vim, Acta2"	Mesangial cells	Tissue	Kidney	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Mesangial cells	"Gsn, Dcn"	Mesangial cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Mesangial cells	Nt5e	Mesangial cells	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	NA	"Hmgb2, Lubb5, Stmn1"	Cycling	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Novel	"Dnm3, Nfat5"	Novel	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	P. tubule	"Ghr, Drand1b, Dab2, Cyp7b1, RP24-362L9.2"	P. tubule	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Principal cells	"Hsd11b2, Aqp4, Aqp2"	Principal cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129801
Mouse	Principal cells	"Scnn1g, Aqp2"	Principle cells of collecting duct in cortex	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Principal cells	Aqp2	Principle cells of collecting duct in medulla	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Proliferating cells	Mki67	Proliferating cells	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Proximal cells	Vil1	Proximal brush border cells	Tissue	Kidney	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Renal corpuscle cells	Cldn1	Renal corpuscle cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129798
Mouse	Renin-producing cells	Ren1	Renin-producing cells	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	S3 segment of proximal tubule	"Lrp2, Slc16a9"	S3 segment of proximal tubule	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Starburst amacrine cells	"Megf10, Sox2, Isl1, Slc18a3"	Starburst amacrine cells	Cell line	Kidney	31812516	Neuron	Binary Fate Choice between Closely Related Interneuronal Types Is Determined by a Fezf1- Dependent Postmitotic Transcriptional Switch	GSE132555
Mouse	Tal	"Slc12a1, Umod"	Tal	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	T cells	"Ifng, Nkg7, Ccl4, Ccl5"	T helper 1 effector cells	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	T cells	"Il17a, Tmem176a, Tmem176b"	T helper 17 cells	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	Thin limb of loop of henle cells	"Aqp1, Sptssb"	Thin limb of loop of henle cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129799
Mouse	Tub epithelial	Slc22a12	Tub epithelial	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Type a intercalated cells of collecting duct	Kit	Type a intercalated cells of collecting duct	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Type B intercalated cells of collecting duct	Slc26a4	Type B intercalated cells of collecting duct	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Ureteric bud tip cells	Slco4c	Ureteric bud tip cells	Tissue	Kidney	33420268	Sci Rep	Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cell	"Ret, Wnt11, Wnt9b, Gata3"	Ureteric epithelium	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Urothelium	Upk1b	Urothelium	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Arterial cells	"Kdr, Cdh5"	Arterial cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129803
Mouse	Stromal cells	"MEIS1, Gdnf"	Stromal cells	Tissue	Kidney	29183737	Dev Biol	Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf	GSE104396
Mouse	Fibroblasts	"Plac8, Cdca3"	Fibroblasts	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Dendritic cells	"Ptprc, Adgre1, Cx3cr1, Ppt1"	CDC1	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Dendritic cells	"Ptprc, Adgre1, Sirpa, Cx3cr1"	CDC2	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Endothelial cells	Plvap	Fenestrated endothelial cells	Tissue	Kidney	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Collecting duct cells	"Tmem213, Sfc26a4, Atp6v1g3"	Collecting duct-3	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Collecting duct cells	Hsd11b2	Collecting duct-2	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Collecting duct cells	"Hsd11b2, Agp2"	Collecting duct-1	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Collecting duct cells	Upk1b	Collecting duct root cells	Tissue	Kidney	33420268	Sci Rep	Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney	GSE108291
Mouse	Nephron	"Cdh16, Mal, Spp1, Spint2"	Distal nephron	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Nephron	"Cdh16, Mal, Spp1, Spint2"	Distal nephron	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cells	Slc12a3	Ductal epithelial cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Nephron	Wnt4	Early nephrons	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Endothelial cells	"Nrp1, Kdr"	"Endothelial, vascular, and descending loop of henle"	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	B cells	"Cd79a, B220"	B cells	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Dendritic cells	"Snx22, Batf3"	Dendritic cells	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Dendritic cells	"Snx22, Batf3"	Dendritic cells	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Lymphocyte cells	Il7r	Innate lymphoid cells (ILCs)	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Natural killer (NK) cells	Gzma	Natural killer (NK) cells	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Immune cells	Tryobp	Immune cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Immune cells	Tryobp	Immune cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Epithelial cells	Cldn1	Glomerular parietal epithelial cells	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Epithelial cells	"Epcam, Umod, Scnn1a, Slc12a1, Ppp1r1a, Sostdc1"	Kidney loop of henle epithelial cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Macrophages	"C1qa, C1qb"	Macrophages	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Macrophages	"Ccr2, Itgam, Plac8, Lyz2, Cebpb"	Infiltrating macrophages	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Macrophages	"Ccr2, Itgam, Plac8, Lyz2, Cebpb"	Infiltrating macrophages	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Macrophages	"Apoe, Lyz, Ctsb, Trem2, Cx3cr1, Lamp1, Lyz2, Fcgr3"	Inflammatory macrophages	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	Macrophages	"Ptprc, Adgre1, Fyb"	M1 macrophages	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Macrophages	C1qc	Macrophages	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129804
Mouse	B cells	Cd79a	B cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129806
Mouse	Fibroblasts	Dcn	Fibroblasts	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129807
Mouse	Natural killer (NK) cells	Tyrobp	Natural killer (NK) cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129807
Mouse	T cells	Thy1	T lymphocytes cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129805
Mouse	Muscle cells	Cnn1	Vascular smooth muscle cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129807
Mouse	Macrophages	"Ptprc, Adgre1, Mertk, Stab1"	M2-like macrophages	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Macrophages	"Axl, Apoe, C1ga"	Macro-1	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Macrophages	Arf1	Macro-2	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Macrophages	Itgam	Macrophages	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Macrophages	"St18, Spi1, Hdac9"	Macrophages	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	B cells	"Cd79a, Cd22, Cd19"	B cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Endothelial cells	"Pecam1, Podxl"	Capillary endothelial cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Natural killer (NK) cells	Nkg7	Natural killer (NK) cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Macrophages	"Adgre1, Fcgr1, C1qc"	Resident macrophage	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Macrophages	"Cd14, Cd68, Csf1r, Fcgr4, Cst3"	Resident macrophages	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	T cells	"Ccr7, Lef1, Satb1, Sell"	Naive T cells	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	Nephron	SIX2	Nephron progenitors	Tissue	Kidney	29183737	Dev Biol	Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf	GSE104396
Mouse	Nephron	SIX2	Nephron progenitors	Tissue	Kidney	29183737	Dev Biol	Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf	GSE104396
Mouse	Nephron	"Cited1, Six2, Pax2, Meox1"	Nephron progenitors	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Nephron	"Cited1, Six2, Pax2, Meox1"	Nephron progenitors	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Nephron	"Rspo3, Cited1, Crym, Six2, Eya1, Spock2"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Rrm2, Top2a, Hist1h2ap"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Hist1h2bc, Ccnb2, Cenpa, Hmgb1"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Hist1h2bc, Fam132a, Frzb, Snap91"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Notch2, Cbx3, Spry2"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Rrm2, Top2a, Notch2, Cbx3, Spry2"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Wnt4, Tmem100, Lhx1, Jag1, Pax8, Pou3f3"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	"Col3a1, Meg3, Lgals1, Foxd1, Meis1"	Nephron progenitors	Cell line	Kidney	32554463	J Biol Chem	The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in Mouse	GSE110925 and GSE144384
Mouse	Nephron	Six2	Nephron progenitors	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Nephron	Six1	Nephron progenitors	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Neutrophils	"S100a8, S100a9"	Neutrophils	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Neutrophils	Lcn2	Neutrophils	Tissue	Kidney	30948627	J Am Soc Nephrol	Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species	GSE128993
Mouse	Neutrophils	"Ptprc, Lcn2, G0s2, S100a8"	Neutrophils	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Neutrophils	"S100a9, S100a8, Retnlg"	Neutrophils	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Epithelial cells	Ncam1	Parietal epithelial cells	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Pericytes	"Thsd4, Pdgfrb, Myh11"	Pericytes	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Plasmacytoid dentritic cells	"Irr8, Siglecn"	Plasmacytoid dentritic cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Plasmacytoid dentritic cells	"Siglech, Cd300c"	Plasmacytoid dentritic cells	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Podocytes	"Nphs1, Nphs2"	Podocytes	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Podocytes	"Podxl, Wt1, Mme"	Podocytes	Tissue	Kidney	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Podocytes	"Mafb, Nphs1"	Podocytes	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Podocytes	"Mafb, Nphs1"	Podocytes	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Podocytes	Nphs2	Podocytes	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Podocytes	"Nphs1, Nphs2"	Podocytes	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Podocytes	Slc3a1	Podocytes	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Podocytes	"Nphs1, Nphs2"	Podocytes	Tissue	Kidney	33420268	Sci Rep	Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney	GSE108291
Mouse	Endothelial cells	"Flt1, Eln"	Endothelial cells	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Fibroblasts	Pdgfrb	Fibroblasts	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Proximal tubular cells	"Slc27a2, Lrp2"	Proximal tubular cells	Tissue	Kidney	29622724	Science	Single-cell transcriptomics of the Mouse kidney reveals potential cellular targets of kidney disease	NA
Mouse	Proximal tubular cells	"Spp2, Lrp2"	Proximal tubular cells	Tissue	Kidney	31689386	Dev Cell	"Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney"	GSE129798
Mouse	Proximal tubular cells	"Gatm, Spp2, Gpx3, Cyr61, Lmo3, Zbtb20, Mox, Aldob, Ass1"	Proximal tubule5	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Proximal tubular cells	"Gatm, Spp2, Gpx3, Mox, Aldob, Ass1"	Proximal tubule4	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Proximal tubular cells	"Gatm, Spp2, Gpx3, Cyr61, Lmo3, Zbtb20, Mox, Aldob, Ass1"	Proximal tubule3	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Proximal tubular cells	"Gatm, Spp2, Gpx3, Mox, Aldob, Ass1"	Proximal tubule2	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Proximal tubular cells	"Acy3, Naosa, Kap"	Proximal tubule1	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Proximal tubular cells	Npt2a	Proximal tubular cells	Tissue	Kidney	33159963	Kidney Int	Targeting fibroblast growth factor 23-responsive pathways uncovers controlling genes in kidney mineral metabolism.	GSE142113
Mouse	Proximal tubular cells	"Slc22a6, Kap"	Proximal tubular cells	Tissue	Kidney	33420268	Sci Rep	Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney	GSE108291
Mouse	Proximal tubular cells	"Fbp1, Pck1"	Proximal tubular cells	Tissue	Kidney	32694833	Nat Metab	Altered proximal tubular cell glucose metabolism during acute kidney injury is associated with mortality	GSE151167
Mouse	Proximal tubular cells	"Slc27a2, Slc3a1, Slc5a12"	Proximal tubular cells	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Proximal tubular cells	Slc5a2	Proximal tubular cells 1	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Proximal tubular cells	Cubn	Proximal tubular cells 3	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Proximal tubular cells	Pck1	Proximal tubular cells 4	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Proximal tubular cells	"Knl1, Prc1"	Proximal tubular cells 5	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Proximal tubular cells	Slc5a2	Proximal tubules s1 segment	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Proximal tubular cells	Slc34a1	Proximal tubules s2 segment	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Proximal tubular cells	"Aqp1, Slc7a13"	Proximal tubules s3 segment	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	T cells	"Ikzf2, Klrg1, Foxp3, IL2ra"	Regulatory T cells (Treg)	Tissue	Kidney	32051345	JCI Insight	Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	"E-MTAB-7957, E-MTAB-7961, and E-MTAB-8002"
Mouse	Endothelial cells	"Pecam1, Zeb1"	Endothelial cells	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Immune cells	"Adam33, Nos2"	Immune cells	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Mesenchymal cells	"Meis1, Ctgf"	Mesenchymal cells	Tissue	Kidney	32673289	JCI Insight	Fluid-electrolyte homeostasis requires histone deacetylase function	GSE148354
Mouse	Stromal cells	"Col3a1, Foxd1"	Stromal cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Stromal cells	"Col3a1, Foxd1"	Stromal cells	Tissue	Kidney	31118232	Development	Single cell analysis of the developing Mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk	GSE108291
Mouse	Stromal cells	Foxd1	Stromal progenitors	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	B cells	"lgkc, Cd79a, Ighm"	B cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Dendritic cells	"Cst3, Lso1, H2-Aa"	Conventional dendritic cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Endothelial cells	"Emcn, Tm4sf1, Lkpc1"	Endothelial cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Myeloid cells	"Cst3, Lso1, H2-Aa, Cybb, Gngt2, Cenbbb, Lyz2, Ifrp3"	Monocytes/macrophages	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Mast cells	"Ccl3, ler3, Ccl4"	Mast cells_basophils	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Natural killer (NK) cells	"Gzma, Klra4"	Natural killer (NK) cells	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Lymphocyte cells	"Ltb, Trpc2, Ccf5, Cd30, Nkg7"	T lymphocyte-1	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	Lymphocyte cells	"Ltb, Trpc2, Ccf5, Cd30"	T lymphocyte-2	Organoids	Kidney	32970632	JCI Insight	Single cell transcriptomics of Mouse kidney transplants reveals a myeloid cell pathway for transplant rejection	GSE157292
Mouse	T cells	Cd3e	T cells	Tissue	Kidney	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	T cells	Cd247	T cells	Tissue	Kidney	32571916	Proc Natl Acad Sci U S A	Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.	GSE139107
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Kidney	33197428	Dev Biol	Molecular detection of maturation stages in the developing kidney	GSE149134
Mouse	Dendritic cells	"Cd209a, Cd11b"	DC 11b+	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Dendritic cells	"Cd24a, Clec9a"	DC 11b-	Tissue	Kidney	33301705	Cell Metab	The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation	GSE156686
Mouse	Epithelial cells	"Acta2, Lta, Umod"	Tubular epithelial cells	Organoids	Kidney	32938648	J Am Soc Nephrol	"Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease"	NA
Mouse	Macrophages	"Spacrc, Vsig4"	CX3CR1+ lining marcophages	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Early articular chondrocytes	Col22a1	Early articular chondrocytes	Tissue	Knee	31522976	Stem Cell Reports	Lgr5 and Col22a1 Mark Progenitor Cells in the Lineage toward Juvenile Articular Chondrocytes	GSE130919
Mouse	Interzones	"Gdf5, Wnt9a"	Interzones	Tissue	Knee	31522976	Stem Cell Reports	Lgr5 and Col22a1 Mark Progenitor Cells in the Lineage toward Juvenile Articular Chondrocytes	GSE130919
Mouse	Stmn1+ proliferating cells	"Stmn1, Ube2c, Birc5"	STMN1+ proliferating cells	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Chondrocytes	"Col2a1, Acan, Sox9"	Chondrocytes	Tissue	Knee	31935848	Int J Mol Sci	Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mouse.	NA
Mouse	Progenitor cells	Lgr5	Highly proliferative progenitor cells	Tissue	Knee	31522976	Stem Cell Reports	Lgr5 and Col22a1 Mark Progenitor Cells in the Lineage toward Juvenile Articular Chondrocytes	GSE130919
Mouse	Macrophages	"Aqp1, Fxyd2"	AQP1+ interstitial macrophages	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Macrophages	"H2-Eb1, H2-Ab1"	MHCII interstitial marcophages	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Osteoblasts	"Acp5, Ctsk"	ACP5+ osteoclast precursors	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Macrophages	"Ccl8, Ccl7"	RELM-alpha+ interstitial marcophages	Tissue	Knee	31391580	Nature	Locally renewing resident synovial macrophages provide a protective barrier for the joint.	GSE134691
Mouse	Endothelial cells	"Pecam1, Esam, Cav1, Igfbp7, Sparcl1"	Endothelial cells	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Endothelial cells	"Esam, Cav1"	Endothelial cells	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Epithelial cells	"Ecad, Epcam, Krt8, Krt18"	Epithelial cells	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Epithelial cells	"Krt8, Epcam"	Epithelial cells	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Erythrocytes	"Hba2, Snca, Alas2"	Erythrocytes	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Immune cells	"Coro1a, Lsp1, Cd52a, Lat"	Lymphocytes/mast cell	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Myeloid cells	"Coro1a, Lsp1, Cd14, Cd68"	Macrophage/monocytes	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Immune cells	"Coro1a, Fcer1g, Apoe, Cd52, Cd68"	Innate immune cells	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Mesenchymal cells	"Ly6a, Mfap5"	Mes1	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Mesenchymal cells	"Ly6a, Mfap5, Gap43"	Mes2	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Mesenchymal cells	"Ly6a, Mfap5, Ndufa4l2, Sec23a"	Mes3	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Mesenchymal cells	"Ly6a, Mfap5, Ckap2"	Mes4	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Neural cells	"Vim, Lum, Col1a1, Col3a1, Gap43"	Mesenchymal neural crest cells 1	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Neural cells	"Vim, Lum, Col1a1, Col3a1, Gdf10"	Mesenchymal neural crest cells 2	Tissue	Lacrimal gland	28576768	Development	Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland	GSE10010
Mouse	Stem cells	"Lgr5, Mki67"	Proliferating stem cells	Tissue	Large intestine	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Chromaffin cells	"Chga, Chgb"	Chromaffin cells	Tissue	Large intestine	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Enterocytes	"Krt20, Slc26a3"	Enterocytes	Tissue	Large intestine	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Goblet cells	"Atoh1, Spdef"	Goblet cells	Tissue	Large intestine	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Tuft cells	Dclk1	Tuft cells	Tissue	Large intestine	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	"Cd14, Fcgr3, Csf1r, Adgre1"	Macrophages	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	B cells	"Cd79a, Cd79b"	B cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Endothelial cells	"Pecam1, Vwf"	Endothelial cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Stromal cells	"Lum, Dcn"	Mesenchymal stromal cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Monocytes	"Cd14, Fcgr3"	Monocytes	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Natural killer (NK) cells	"Gzma, Nkg7"	Natural killer (NK) cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Muscle cells	"Myh11, Cnn1, Acta2, Tagln"	Smooth muscle cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Red cells	"Gypa, Alas2"	Red blood cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	T cells	"Cd3d, Cd3g, Rora, Gata3"	T cells	Tissue	Large vessels	32166394	Cell Mol Life Sci	Cellular and Molecular Life Sciences	"GSE140811, GSE117963, GSE109774"
Mouse	Eritrocytes	Hbb-bs	Eritrocytes	Tissue	Left ventricle	31399586	Nat Commun	WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling	GSE133015
Mouse	Cardiomyocytes	Ttn	Cardiomyocytes	Tissue	Left ventricle	31399586	Nat Commun	WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling	GSE133015
Mouse	Endothelial cells	"Aplnr, Pecam1"	Endothelial cells	Tissue	Left ventricle	31399586	Nat Commun	WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling	GSE133015
Mouse	Fibroblasts	Lum	Fibroblasts	Tissue	Left ventricle	31399586	Nat Commun	WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling	GSE133015
Mouse	Immune cells	"Ccr2, Cd163, Ptprc"	Immune cells	Tissue	Left ventricle	31399586	Nat Commun	WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling	GSE133015
Mouse	San	"Hcn4, Isl1, Shox2, Tbx3"	San	Tissue	Limb	31284824	Circ Res	Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution	GSE132658.
Mouse	Hematopoietic cells	"Fcgr1, Cd33, Cd48"	Hematopoietic cells	Tissue	Limb buds	32386547	Cell	Unblending of Transcriptional Condensates in Human Repeat Expansion Disease.	GSE128818
Mouse	Myoblasts	"Myod1, Myog, Tnnt2"	Myoblasts	Tissue	Limb buds	32386547	Cell	Unblending of Transcriptional Condensates in Human Repeat Expansion Disease.	GSE128818
Mouse	Erythrocytes	"Hbb-bh1, Hbb-bs, Hba-a2"	Erythrocytes	Tissue	Limb buds	32386547	Cell	Unblending of Transcriptional Condensates in Human Repeat Expansion Disease.	GSE128818
Mouse	Stem cells	Atxn1	Mesenchymal stem cells	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Satellite cells	Vcam1	Satellite cells	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	Cd19	B cells	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Myeloid cells	Itgam	Monocytes/macrophages	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	Cd3g	T cells	Tissue	Limb muscle	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Canonical biliary	"Epcam, Krt7, Krt19, Aqp1, Aqp4, Cldn7"	Canonical biliary	Tissue	Liver	30500539	Cell	Inflammatory Cytokine TNFalpha Promotes the Expansion of Primary Hepatocytes in 3D Culture	"GSM3040892, GSM3040898, GSM3040899"
Mouse	Clec4f macs	"Mafb, Fcgr1, Csf1r, Sirpa, Zeb2, H2-Aa"	Clec4f macs	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Dividing cells	Top2a	Dividing cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Erythrophagocytosis	"Hba-a1, Marco"	Erythrophagocytosis	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	Eythrocytes	"Alas2, Hbb-bt, Hbb-bs, Hba-a2, Hba-a1"	Eythrocytes	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Hepatocyte precursors	AFP	Hepatocyte precursors	Tissue	Liver	33208554	JCI Insight	Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration	"GSE158866 [scRNA-Seq], and GSE158874 [scATAC-Seq]"
Mouse	Immature cholangiocytes	"Sox9, Hnf1b"	Immature cholangiocytes	Tissue	Liver	33208554	JCI Insight	Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration	"GSE158866 [scRNA-Seq], and GSE158875 [scATAC-Seq]"
Mouse	Inflammatory cells	Opn	Inflammatory cells	Tissue	Liver	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Insulin cells	Alb	Insulin liver cells	Tissue	Liver	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Kc3-control	"Cxcl13, Wfdc17, Marco, Ifitm2, Gm10116, Vsig4, Apoc1, Timd4, Fabp7, Cfp, Folr2, Ccl6, Aif1, AW112010, Blvrb, Clec1b, Fcgr4, Ninj1, Cd302, Ctla2b"	Kc3-control	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Kc-h (healthy)	"Cd163, Marco, C6, Hmox1, Fcna, Slc40a1, Sdc3, C4b, Timd4, Tnfaip2, Mrc1, Ptprj, Adgre4, Itgal, BC005537, Vcam1, Cd44, Cxcl13, Paqr9, Atp1b3"	Kc-h (healthy)	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Kc-n (nash)	"Folr2, Cd5l, Ear2, Apoc1, Clec1b, C1qb, Ctsd, Fabp7, Il18bp, Pltp, Aif1, Apoe, Wfdc17, Igf1, Trem2, Clec4n, Lpl, Clec4f, Mmp12, Ccl24"	Kc-n (nash)	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Stem cells	Cd34	Keratinocyte stem cells	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Kn-rm-nash	"Cx3cr1, Ms4a7, Trem2, Cd63, Apoe, H2-Eb1, Cd74, H2-Ab1, H2-Aa, Gpnmb, Hexb, Cd9, Clec4b1, Bcl2a1b, H2-M2, Cxcl14, Pf4, Mmp12, Fabp5, Cd207"	Kn-rm-nash	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Ly6chi-rm	"Chil3, Fn1, S100a4, Hp, F13a1, Gm9733, F10, Emb, Ccr2, S100a6, Mcemp1, Sirpb1c, Ms4a4c, Lyz2, Ly6c2, Coro1a, Ms4a6b, Ccl9, Ifitm6, Plac8"	Ly6chi-rm	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Ly6clo-rm	"Cd209a, Klrd1, S100a4, Flt3, Cbfa2t3, Napsa, S100a6, Lsp1, Cd7, Tppp3, S100a11, Vim, Gm2a, Crip1, H2-Oa, Coro1a, Fxyd5, S100a10, Lgals1, Tagln2"	Ly6clo-rm	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Mig.cdc2s	"H2-Aa, Ccr7"	Mig.cdc2s	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Pdc-control	"Siglech, Cox6a2, Ly6d, Klk1, Cd209d, Cd300c, Smim5, Ccr9, D13Ertd608e, Atp1b1, Klk1b27, Sell, Ly6c2, Rpgrip1, Rnase6, Dnajc7, Tcf4, Lgals1, Bst2, Irf8"	Pdc-control	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Pdc-nash	"Siglech, Ccr9, Atp1b1, Cd300c, Cox6a2, Upb1, Pacsin1, Smim5, Klk1, Sell, Ly6d, Cd209d, Ly6c2, Rnase6, Tsc22d1, Irf8, Dnajc7, Bst2, Lgals1, Plac8"	Pdc-nash	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Pdcs	"Ly6c2, Irf8, Clec10a, Zeb2, Tcf4, Siglech, Cd7"	Pdcs	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Proliferating cells	"Ccna2, Top2a, Mki67, Cdk1, Cenpm"	Proliferating cells	Tissue	Liver	30500539	Cell	Inflammatory Cytokine TNFalpha Promotes the Expansion of Primary Hepatocytes in 3D Culture	"GSM3040892, GSM3040898, GSM3040899"
Mouse	Keratinocytes	"Stmn1, Top2a, Ube2c, Birc5, 2810417H13Rik, Ccnb2, Mki67, Cdca3, Lockd, Cdk1, Smc2, Cenpa, Cks2, Cks1b, Hmgb2, H2afx, Hist1h2ap, Smc4, Tubb5, Tuba1b"	Proliferating keratinocytes	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Keratinocytes	"Mafb, Adgre1, Clec4f, Csf1r, Cd51, Sirpa, Zeb2"	Proliferating keratinocytes	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Stellate cell	"Fcna, Angptl6, Fgf21"	Resting hepatic stellate cell	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Stellate cell	"Fcna, Angptl6, Fgf21"	Resting hepatic stellate cell	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Retinoblastima cells	"Hbb-bt, Hbb-bs, Hba-a2, Hba-a1, Bpgm, Snca"	Retinoblastima cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Stellate cells	Dcn	Stellate cells	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Stellate cells	"Dcn, Colec11, Ecm1, Cxcl12, Sod3, Angptl6, Rgs5, Reln, Tmem56, Rbp1, G0s2, Rarres2, Acta2, Tagln"	Stellate cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Progenitor cells	"Yap, Gata6"	Bipotent liver progenitors	Tissue	Liver	33208554	JCI Insight	Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration	"GSE158866 [scRNA-Seq], and GSE158873 [scATAC-Seq]"
Mouse	Epithelial cells	Opn	Biliary epithelial cells	Tissue	Liver	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Dendritic cells	"Irf8, Itgax, Xcr1, Clec9a, H2-Aa"	CDC1	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Dendritic cells	"Itgam, H2-Aa, Zeb2"	CDC2	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Cholangiocytes	Sox9	Cholangiocytes	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Cholangiocytes	"Krt7, Krt19, Tff2, Scgb3a1, Fxyd2, Defb1"	Cholangiocytes	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Cholangiocytes	Epcam	Cholangiocytes	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	B cells	"Cd79a, Cd79b, Cd74, Cd19"	Circulating B cells	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Pecam1, Nrp1, Kdr, Oit3"	Endothelial cells	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Natural killer T (NKT) cells	"Zap70, Il2rb, Nkg7, Cxcr6, Gzma"	Natural killer T (NKT) cells	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	CD4 T cells	"Cd3, Cd4"	CD4 T cells	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	CD8 T cells	"Cd3, Cd8"	CD8 T cells	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Dendritic cells	"Cd74, H2-Ab1, Ccl22, Ccl17"	Dendritic cells	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Monocytes	"Csf1r, Itgam"	Monocytes	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Natural killer (NK) cells	"Cd3, Ncr1"	Natural killer (NK) cells	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	B cells	Cd79a	B cells	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Dendritic cells	Siglech	Dendritic cells	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Natural killer T (NKT) cells	"Klrb1c, Cd3g"	Natural killer T (NKT) cells	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Epithelial cells	"Nes, Gja1, Cdh1"	Epithelial mesenchymal transition	Tissue	Liver	31514486	Cells	Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury	NA
Mouse	Myofibroblasts	"S100a6, Acta2, Tglna, Col1a1, col3a1, Col6a3"	Activated myofibroblasts  I	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Slpi, C3, Saa3, Cd74"	Activated myofibroblasts II	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Ap1, Jund, FosB"	Activated myofibroblasts III	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Mgp, Fbln1, Gas6"	Activated myofibroblasts IV	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Acta2, Tglna, Col1a1, col3a1, Col6a3"	Activated myofibroblasts I	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Slpi, C3, Saa3, Cd74"	Activated myofibroblasts II	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Ap1, Jund, FosB"	Activated myofibroblasts III	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Myofibroblasts	"S100a6, Mgp, Fbln1, Gas6"	Activated myofibroblasts IV	Organoids	Liver	31137713	MDPI cells	Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis	NA
Mouse	Hepatic stellate cells	Dcn	Hepatic stellate cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Hepatic stellate cells	NA	Hepatic stellate cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Hepatic stellate cells	NA	Hepatic stellate cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Hepatic stellate cells	"Lrrn3, Gja1, Sprn, Inmt, Adm, Robo2, Vcam1, Loxl1, Tsc22d1, Htra3, Sox4, Sectm1a, Adamts5, Slc43a3, Apoc1, Gm13889, Qpct, Lpar1, Podn, Gem, Ackr4, Bmyc, Fcna, Lum, Ano1, Adamtsl2, Rspo3, Spon2"	Hepatic stellate cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Hepatic stellate cells	"gfbp3, Sparc, Gcgr, Ndufa4l2, Tnfrsf11b, Tagln, Rgs4, Ttyh1, Clca3a1, Clec4g, Rasl11a, Il34, Tmem178, Col14a1, Heyl, Prss23, Myl9, Tpm2, Lama1, Susd2, Fam84a, Gns, Alpl, Bcr, Pdgfrb, Klhl23, Mest, Ckb, Gpc6, Cyp4b1, Itgb3, Tbx2, Disp2, Serpina3g, Ccl2, Fhl2, Crip1, Rem1, Hilpda, Hsd11b1, Gja4, M"	Hepatic stellate cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Hepatic stellate cells	"Col1a1, Col11a2, Acta1, Tagln, Col13a1, Rbp1, Sparc"	Hepatic stellate cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Hepatic stellate cells	"Dcn, Cxcl12, Colec11, Rbp1, Lum, Mmp2, Col1a1, Col1a2, Col3a1, Lrat, Rgs5, Hand2, Reln, Sod3, Ifitm1"	Hepatic stellate cells	Tissue	Liver	32145072	Hepatology	Transcriptional Dynamics of Hepatic Sinusoid-Associated Cells After Liver Injury	NA
Mouse	Hepatic stellate cells	Lrat	Hepatic stellate cells	Tissue	Liver	32455750	Pharmaceutics	Osteoprotegerin is More than a Possible Serum Marker in Liver Fibrosis: A Study into its Function in Human and Murine Liver	NA
Mouse	Hepatic stellate cells	Dcn	Hepatic stellate cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK7 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Hepatic stellate cells	"Col1a1, Acta2"	Hepatic stellate cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Epithelial cells	"Krt8, Krt18, Tjp1"	Hepatocyte epithelial cells	Tissue	Liver	30500539	Cell	Inflammatory Cytokine TNFalpha Promotes the Expansion of Primary Hepatocytes in 3D Culture	"GSM3040892, GSM3040898, GSM3040899"
Mouse	Hepatocytes	"Alb, Ttr, Apoa1, Serpina1c, Cyp2e1, Glul, Oat, Gulo"	PC hepatocytes	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hepatocytes	"Alb, Ttr, Apoa1, Serpina1c, Cyp2f2, Pck1, Hal, Cdh1"	Periportal PP hepatocytes	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hepatocytes	"Alb, Ttr, Apoa1, Serpina1c, Ass1, Hamp, Gstp1, Ubb"	Midlobular (ML) hepatocytes	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hepatocytes	"Alb, Apoa1, Ttr, Serpina1c, Hnf4a, Fga, Fn1, Rbp4, Glul, Slc1a2"	Hepatocytes	Tissue	Liver	30500539	Cell	Inflammatory Cytokine TNFalpha Promotes the Expansion of Primary Hepatocytes in 3D Culture	"GSM3040892, GSM3040898, GSM3040899"
Mouse	Hepatocytes	Apoc3	Hepatocytes	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Hepatocytes	Alb	Hepatocytes	Tissue	Liver	31514486	Cells	Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury	NA
Mouse	Hepatocytes	Mup3	Hepatocytes	Tissue	Liver	31514486	Cells	Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury	NA
Mouse	Hepatocytes	Alb	Hepatocytes	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Hepatocytes	"Apoa1, Apob, Pck1, G6pc, Ttr"	Hepatocytes	Tissue	Liver	31784108	Immunity	Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function	"GSE123688,"
Mouse	Hepatocytes	"Ambp, Clu, Serpina1c, Ttr, Serpina1a, Serpina1e, Mup7, Rbp4, Serpina1b, Alb, Bhmt, Mup11, Apoc3, Spp1, Serpina3k, Mup3, Fabp1, Mup20, Apoa1, Apoa2"	Hepatocytes	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Hepatocytes	"Dcn, Apoa2, Ttr, Alb"	Hepatocytes	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	Hepatocytes	"Alb, Ttr, Ambp, Rbp4, Cyp2e1, Spp1"	Hepatocytes	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Hepatocytes	Gulo	Hepatocytes 1	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK2 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Hepatocytes	Hsd17b13	Hepatocytes 2	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK3 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Hepatocytes	Pecr	Hepatocytes 3	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK4 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Hepatocytes	Mlxipl	Hepatocytes 4	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK5 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Natural killer (NK) cells	"NK1.1, NKp46, Eomes"	Natural killer (NK) cells	Tissue	Liver	31393266	eLife	Toxoplasma gondii infection drives conversion of NK cells into ILC1-like cells.	GSE124577
Mouse	B cells	Ebf1	B cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Dendritic cells	Irf8	Dendritic cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Endothelial cells	Stab2	Endothelial cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Endothelial cells	Stab2	Endothelial cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Endothelial cells	Stab2	Endothelial cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	B cells	Jchain	Plasma cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Keratinocytes	"Mafb, Adgre1, Clec4f, Csf1r, Cd51, Sirpa, Zeb2, H2-Aa"	Keratinocytes	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Kupffer cells	"Emr1, Clec4f, Cd68, Irf7"	Kupffer cells	Tissue	Liver	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Kupffer cells	"Clec4f, Spic, Marco, Vsig4, Cpvl, Cd163, Cd68"	Kupffer cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Kupffer cells	"Clec4f, Csf1r, C1qc, C1qa, C1qb"	Kupffer cells	Tissue	Liver	31784108	Immunity	Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function	"GSE123688,"
Mouse	Kupffer cells	"Clec4f, Cd68, Adgre1, Ptprc"	Kupffer cells	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	Leukocytes	Lyz2	Leukocytes	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Leukocytes	Lyz2	Leukocytes	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Liver	31514486	Cells	Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury	NA
Mouse	Macrophages	"S100a11, Ccr2, Itgam, S100a6"	Early recruited macrophages	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	Macrophages	"Epor, Klf1"	Erythroblastic island macrophages	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	Macrophages	"Csf1r, Itgam"	Macrophages	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Macrophages	Adgre1	Macrophages	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Macrophages	"Cd74, C1qc, Wfdc17, Cd5l, Lyz2, Vsig4, C1qb, Tyrobp, Clec4f, Cd44, Aif1, Adgre1, Spi1"	Kupffer cell/monocyte_derived macrophages (kc/mdms)	Tissue	Liver	32145072	Hepatology	Transcriptional Dynamics of Hepatic Sinusoid-Associated Cells After Liver Injury	NA
Mouse	Macrophages	Adgre1	Kupffer cell/monocyte_derived macrophages (kc/mdms)	Tissue	Liver	32455750	Pharmaceutics	Osteoprotegerin is More than a Possible Serum Marker in Liver Fibrosis: A Study into its Function in Human and Murine Liver	NA
Mouse	Macrophages	Csf1r	Macrophages	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Macrophages	Csf1r	Macrophages	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Macrophages	Csf1r	Macrophages	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	Mesenchymal cells	NA	Mesenchymal cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Mesenchymal cells	NA	Mesenchymal cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Mesenchymal cells	NA	Mesenchymal cells	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Mesenchymal cells	"Abca8a, Ablim1, Ace, Ackr3, Acvrl1, Adamts2, Adcy7, Adk, Aebp1, Aes, Aff3, Ahnak, Ahnak2, Akap12, Ang, Angptl4, Anpep, Anxa5, Arf4, Arrdc3, Aspn, Atf5, Atxn10, B3gnt9, Bicc1, Bmp4, Boc, C1qtnf7, C3, C4b, C7, Camk2n1, Capg, Ccdc80, Cd302, Cd34, Cd63, Cd9, Cdon, Cebpd, Celf2, Ces2g, Cfh, Cgnl1, Cilp"	Fibroblast	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Mesenchymal cells	"1700025G04Rik, A230050P20Rik, Aard, Abcc9, Abcg1, Abi3bp, Ablim2, Acaa2, Acap1, Acsl5, Actn4, Acvr2a, Adamts13, Adamtsl2, Adamtsl4, Adap2, Adap2os, Add3, Adora2a, Adra2b, Afap1l2, Agtr1a, Aldh2, Angptl2, Angptl6, Ank3, Ano1, Anxa2, Apoc1, Apoe, Apold1, App, Arap2, Arhgap24, Arhgap42, Arhgd"	Hepatic stellate cell	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Mesenchymal cells	"Abr, Acta2, Actb, Actg2, Actn1, Adcy5, Adcy6, Adcy9, Amigo2, Aoc3, Arhgap1, Arhgef2, Arid5a, Arl4d, Asap2, Asb2, Aspn, Atp1a2, Atp1b2, Atp2a2, Atp2a3, Atp2b4, Atp5a1, Atp5b, Atp5c1, Atp5d, Atp5e, Atp5g3, Atp5h, Atp5j, Atp5j2, Atp5k, Atp5l, Atp6v0e2, Atpif1, AW549542, Axl, B3gnt2, Bcam, Blmh, Bt"	Vascular smooth muscle cell	Tissue	Liver	31722201	Cell Rep	Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis	NA
Mouse	Macrophages	Ms4a6c	Macrophages	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	B cells	"Cd79a, Cd38, Igll1, Cd19, Cd79b"	B cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Endothelial cells	"Ushbp1, Oit3, F8, Bmp2, Mmrn2"	Endothelial cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Myeloid cells	"Cd68, Ccr2, Ly6c2, Lyz1, Lyz2"	Monocytes/macrophages	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Natural killer (NK) cells	"Nkg7, Cd3e-"	Natural killer (NK) cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Natural killer T (NKT) cells	"Cd3e, Nkg7"	Natural killer T (NKT) cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Macrophages	"Lyz2, Apoe, Fn"	Macrophages	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Endothelial cells	"Kdr, Egflfl7, Igfbp7, Aqp1"	Endothelial cells	Tissue	Liver	31784108	Immunity	Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function	"GSE123688,"
Mouse	Basal cells	Krt1	Basal cells	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Basal cells	Krt1	Basal cells	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Stem cells	Top2a	Stem cells	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Stem cells	Top2a	Stem cells	Tissue	Liver	32075962	Nat Commun	Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants	GSE11546
Mouse	Neutrophils	"Retnlg, Lcn2, Mmp9, Hdc, Wfdc21, S100a9, Pglyrp1, Lrg1, S100a8, Mmp8, Mcemp1, Gda, Camp, Ngp, Hp, Slpi, Chil3, S100a11, Anxa1, Ifitm6"	Neutrophils	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Neutrophils	"Csf3r, Cd33"	Neutrophils	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Neutrophils	Csf3r	Neutrophils	Tissue	Liver	30762896	Hepatology	Tissue Repair in the Mouse Liver Following Acute Carbon Tetrachloride Depends on Injury-Induced Wnt/beta-Catenin Signaling	NA
Mouse	Neutrophils	S100a8	Neutrophils	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	Endothelial cells	"Clec4g, Aqp1, Gpihbp1, Ptprb, Fcgr2b, Kdr, Gpr182, Egf17, Cldn5, Sdpr, Lyve1, Stab2, Nrp1, Pde2a, Stab1"	Liver Endothelial cells (LECs)	Tissue	Liver	32145072	Hepatology	Transcriptional Dynamics of Hepatic Sinusoid-Associated Cells After Liver Injury	NA
Mouse	Neutrophils	"Itgam, Ly6g, S100a8, S100a9, Ly6c2"	Neutrophils	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Neutrophils	"Cd11b, Gzma, Prf1, Ncr1, Klra4, Cma1"	Neutrophils	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Monocytes	"Csf1r, Spn, Sirpa, Zeb2"	Pat.monocytes	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Monocytes	Ly6c2	Monocytes	Tissue	Liver	32346042	Scientific Reports	Adaptable haemodynamic Endothelial cellss for organogenesis and tumorigenesis.	NA
Mouse	B cells	"Cd79a, Ms4a1, Ebf1, Fcmr, Cd19, Cd79b, Mzb1, Ly6d, Siglecg, H2-DMb2, H2-Ob, Ltb, Cd2, Gm43603, Ralgps2, Ptprcap, Cd37, Napsa, Cd24a, Foxp1"	B cells	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	B cells	"Derl3, Fkbp11, Eaf2, Tnfrsf17, Pou2af1, Gm43291, Mzb1, Jchain, Creld2, Txndc5, Pdia4, Edem1, Slpi, Xbp1, Sec11c, H13, Sdf2l1, Ssr4, Manf, Hsp90b1"	B cells	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Dendritic cells	"Xcr1, Cd24a, Ifi205, Flt3, Tnni2, Amica1, Naaa, Septin5, H2-Oa, Wdfy4, Cxx1a, Ppt1, Cst3, Plbd1, Tmsb10, Irf8, Lsp1, H2-Aa, H2-Ab1, Gm2a"	DC-1	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Dendritic cells	"Fscn1, Ccr7, Ccl22, Tbc1d4, Il12b, Il4i1, Traf1, Eno3, Zmynd15, Serpinb6b, Gadd45b, Relb, Rogdi, Tspan3, Ccl5, Bcl2a1d, Tmem123, Gyg, Fabp5, Epsti1"	DC-2	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Endothelial cells	"Igfbp7, Aqp1, Ptprb, Gpihbp1, Clec4g, Kdr, Ehd3, Eng, Egfl7, Adgrf5, Timp3, Bgn, Bmp2, Il6st, Tinagl1, Sdpr, Fabp4, Rspo3, Fcgr2b, Dnase1l3"	Liver sinusoidal endothelial cells (lsecs)	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Natural killer T (NKT) cells	"Nkg7, Ms4a4b, Xcl1, Cd3g, Cd3d, Ctsw, Thy1, Gimap3, Lck, Lat, Skap1, Ltb, Klre1, Klrb1c, Gimap4, Ptprcap, Ccl5, Bcl2, Tmsb10, Cd7"	Natural killer T (NKT) cells	Tissue	Liver	32362324	Immunity	Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis	GSE128662
Mouse	Plasma cells	Cox6a2	Plasma cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK6 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Endothelial cells	Ptprb	Liver Endothelial cells	Tissue	Liver	32455750	Pharmaceutics	Osteoprotegerin is More than a Possible Serum Marker in Liver Fibrosis: A Study into its Function in Human and Murine Liver	NA
Mouse	Dendritic cells	Xrc1	Dendritic cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Endothelial cells	Clec14a	Endothelial cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Erythrocytes	Hbb-bt	Erythrocytes	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	B cells	Cd79a	Mature B cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK8 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	Natural killer (NK) cells	"Cd3d, Nkg7"	T cells/Natural killer (NK) cells	Tissue	Liver	32513687	Proc Natl Acad Sci U S A	Hepatocyte-specific TAK1 deficiency drives RIPK9 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.	GSE148859 (71).
Mouse	T cells	"Cd3, Cd4, Foxp3"	Regulatory T cells (Treg)	Tissue	Liver	30447042	Cancer science	Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model	NA
Mouse	Endothelial cells	"Sparc, Kdr, F8, Clec4g"	Endothelial cells	Organoids	Liver	32663195	J Clin Invest	Hemolysis transforms liver macrophages into antiinflammatory erythrophagocytes	GSE145244
Mouse	B cells	"CD79a, Ms4a1, Cd19, H2-Aa"	B cells	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Monocytes	"Fcgr1, Csf1r, Ly6c2, Zeb2"	Monocytes	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	Natural killer (NK) cells	"Ncr1, spn, Jrf8"	Natural killer (NK) cells	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	T cells	Cd3g	T cells	Tissue	Liver	31398325	Mol Cell	Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis	GSE129516
Mouse	T cells	"Cd3e, Cd4, Cd8a"	T cells	Tissue	Liver	31747600	Cell Rep	Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products	GSE128284
Mouse	T cells	CD8	T cells	Tissue	Liver	32161196	JCI Insight	Differentiated agonistic antibody targeting CD137 eradicates large tumors without hepatotoxicity.	GSE144473
Mouse	B cells	"Cd79b, Cd79a, Ms4a1, Siglecg, Fcmr, Cd19, Fcer2a"	B cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Endothelial cells	"Gpihbp1, Aqp1, Clec4g, Dnase1l3, Fabp4, Ptprb, Kdr, Gpr182"	Endothelial cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Endothelial cells	"Lrg1, Inhbb, Thbd, Bhlhe40"	Endothelial cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	T cells	"Cd3e, Cd3d, Cd5, Cd28, Nki67, Stmn1, Pclat"	T cells	Tissue	Liver	32888418	Immunity	Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver	GSE156059
Mouse	T cells	"Cd3e, Cd3g, Cd3d, Lat, Thy1, Cxcr6, Nkg7, Cd4, Cd8b1, Klra4, Ncr1, Gzmb, Lck, Txk, Ms4a4b, Ccl5"	T cells	Tissue	Liver	33106666	Nat Med	Acute liver failure is regulated by MYC- and microbiome-dependent programs	NA
Mouse	Megakaryocytes	"Cd9, Itga2b, Mpl, Pf4, VWF"	Megakaryocytes	Tissue	Liver	33239297	Sci Adv	Epigenetic Regulation of IL-17-Induced Chemokines in Lung Epithelial Cells	GSE160466
Mouse	B cells	"Cd74, H2-aa, H2-eb1, H2-ab1, Igkc, Cd79b"	B cells	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	CD4 T cells	CD4	CD4 T cells	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	CD8 T cells	Cd8a	CD8 T cells	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Dendritic cells	"Icos, Bst2, Siglech, Tcf4, Ctsl"	Dendritic cells	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Lymphocyte cells	"Tbet, Cd127, Cd7, Xcl1"	Innate lymphoid cells (ILCs)	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Natural killer (NK) cells	"S100a9, S100a8, Il1b, Cxcl2"	Natural killer (NK) cells	Tissue	Liver	33391261	Front Immunol	The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution	CRA003280
Mouse	Ciliated tracheobronch	Mlf1	Ciliated tracheobronch	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Lysosomal cell	Lamp-1	Lysosomal cell	Organoids	Lung	31481690	Nat Commun	Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the Mouse lung	GSE94135
Mouse	Mesothelial cells	"Wt1, Msln"	Mesothelial cells	Organoids	Lung	30824323	Immunity	Adventitial Stromal Cells Define Group 2 Innate Lymphoid Cell Tissue Niches	GSE125492
Mouse	Mesothelial cells	Wt1	Mesothelial cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Mesothelial cells	Msin	Mesothelial cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Mesothelial cells	Msln	Mesothelial cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Mlecs (murine lung ecs)	"Cd31, Cd34, Cdh5"	Ecs	Tissue	Lung	32128409	Sci Adv	Sirt7Vascular endothelium-targeted gene therapy rejuvenates blood vessels and extends life span in a Hutchinson-Gilford progeria model.	GSE138975
Mouse	Mlecs (murine lung ecs)	"Cd31, Ly6d, Cd22, Cd81"	B-like	Tissue	Lung	32128409	Sci Adv	Sirt7Vascular endothelium-targeted gene therapy rejuvenates blood vessels and extends life span in a Hutchinson-Gilford progeria model.	GSE138975
Mouse	Mlecs (murine lung ecs)	"Cd31, Cd3d, Cd3e, Cd28"	T-like	Tissue	Lung	32128409	Sci Adv	Sirt7Vascular endothelium-targeted gene therapy rejuvenates blood vessels and extends life span in a Hutchinson-Gilford progeria model.	GSE138975
Mouse	Mlecs (murine lung ecs)	"Cd31,Cd14, Cd68, Cd282"	Macrophages-like	Tissue	Lung	32128409	Sci Adv	Sirt7Vascular endothelium-targeted gene therapy rejuvenates blood vessels and extends life span in a Hutchinson-Gilford progeria model.	GSE138975
Mouse	Monocytes	"Mafb, Mertk, Fcgr1"	Monocyte-derived cells	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Mpp3	"LKS, CD48, CD34"	Mpp3	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	Mpp4	"LKS, CD48, CD34, Flt3"	Mpp4	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	NA	"Ctsg, Elane, Mpo"	MPP3.C3	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	NA	"Sftpc, Lamp3, Lyz2, Abca3, Sftpa1"	ACE2	Tissue	Lung	30913038	JCI Insight	Single-cell RNA sequencing identifies TGF-b as a key regenerative cue following LPS-induced lung injury	GSE113049
Mouse	NA	"Scgb1a1, Scgb3a1, Scgb3a2"	Club	Tissue	Lung	30913038	JCI Insight	Single-cell RNA sequencing identifies TGF-b as a key regenerative cue following LPS-induced lung injury	GSE113049
Mouse	NA	"Foxj1, Ccdc39, Ccdc113"	Ciliated	Tissue	Lung	30913038	JCI Insight	Single-cell RNA sequencing identifies TGF-b as a key regenerative cue following LPS-induced lung injury	GSE113049
Mouse	Nilc2	ST2	Nilc2	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Nilc2	ST2	Nilc2	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Nilc2	ST2	Nilc2	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Pdcs	"Siglech, Tcf4, Ccr9, Bst2"	Pdcs	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Pericytes	Des	Pericyte-like cells	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Plvap ecs	Esm1	Plvap ecs	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Primary Wharton	"Pf4, Itga2b"	Primary Wharton	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	Pulmonary ams	"Siglecf, Itgax, Mrc1, Pparg"	Pulmonary ams	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	T cells	"CD3, CD4, ST2"	Activated T helper 2	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	T cells	"CD3, CD4"	T helper	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Tumor cells	"Nkx2-1, Ncam1, Cas9, Myc, Uchl1, EGFP, Sox2, Insm1, Neurod1"	Tumor cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Type ii pneumocyte	Pdpn	Type ii pneumocyte	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Venous cells	Nr2f2	Venous cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Epithelial cells	"Ager, Pdpn, Cdh1"	Epithelial cells	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Fibroblasts	"Eln, Pdgfra, Col1a1"	Matrix-producing fibroblasts	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Myofibroblasts	Tagln	Myofibroblasts	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Myofibroblasts	"Acta2, Aoc3"	Myofibroblasts	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Muscle cells	Acta2	Smooth muscle cells	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Muscle cells	"SM22alpha, alphaSMA"	Smooth muscle cells	Tissue	Lung	28886382	Cell	Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung	GSE99714
Mouse	Arterial cells	Gja5	Arterial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	AT1 cells	Pdpn	AT1 cells	Tissue	Lung	32989251	Nat Cell Biol	STAT3-BDNF-TrkB signaling promotes alveolar epithelial regeneration after lung injury	GSE132535
Mouse	AT2 cells	Sftpc	AT2 cells	Tissue	Lung	32989251	Nat Cell Biol	STAT3-BDNF-TrkB signaling promotes alveolar epithelial regeneration after lung injury	GSE132535
Mouse	Epithelial cells	Aqp5	ATI cells	Organoids	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	Lymphocyte cells	"Pax5, Irf4"	Lymphoid tfs	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	Lymphocyte cells	"Lck, Rag1, Rag2"	Lymphoid-lineage	Tissue	Lung	29328912	Cell	BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis	GSE98600
Mouse	Basophils	Mcpt8	Basophils	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Basophils	Cd200r3	Basophils	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd163l1, Trdv4, Gzma, Cdk6"	Gamma delta T cell	Tissue	Lung	32848068	Proc Natl Acad Sci U S A	beta2 Integrins differentially regulate gammadelta T cell subset thymic development and peripheral maintenance	NA
Mouse	Epithelial cells	"Scgb1a1, Scgb3a1, Foxj1, Il33"	Bronchial epithelial cells	Organoids	Lung	32963227	Nat Commun	IL-33-ST2 axis regulates myeloid cell differentiation and activation enabling effective club cell regeneration	GSE155261
Mouse	Dendritic cells	"Flt3, Dpp4, Zbtb46, Cd81, Gcsam, Xcr1, Irf8"	Non-migratory cDC1	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 CDCs Acquire Features of CDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Epithelial cells	EpCAM	Epithelial cells	Tissue	Lung	30135312	JCI Insight	CCR10+ epithelial cells from idiopathic pulmonary fibrosis lungs drive remodeling	GSE115982
Mouse	Ciliated cells	Foxj1	Ciliated cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Ciliated cells	Foxj1	Ciliated cells	Organoids	Lung	32963227	Nat Commun	IL-33-ST2 axis regulates myeloid cell differentiation and activation enabling effective club cell regeneration	GSE155261
Mouse	Monocytes	"Ly6c2, Cd62l, Ccr2, Itga4, Cx3cr1"	Circulating monocytes	Tissue	Lung	31744829	Cancer Discov	In Vivo_pigenetic CRISPR Screen Identifies_sf1a_s an Immunotherapeutic Target in_ras-Mutant Lung Adenocarcinoma	NA
Mouse	Monocytes	Fcgr1	Classical monocytes	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Dendritic cells	"Itgax, Cd24a, Cd68"	Dendritic cells	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Endomucin, CD31"	Endothelial cells	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Mesenchymal cells	"Pdgfra, Pdgfrb, Thbs1, syndecan4"	Mesenchymal cells	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	B cells	Cd19	B cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Dendritic cells	Siglech	Dendritic cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Endothelial cells	Cdh5	Endothelial cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Epithelial cells	Epcam	Epithelium progenitors	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Epithelial cells	"Epcam, Akap5"	AT1 cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Epithelial cells	"Epcam, Lamp3"	AT2 cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Epithelial cells	"Epcam, Scgb3a2"	Club cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Epithelial cells	"Epcam, Foxj1"	Ciliated cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Fibroblasts	"Col1a2, Enpp2"	Mooth muscle cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Fibroblasts	"Col1a2, Mfap4"	Matrix fibroblasts	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Fibroblasts	"Col1a2, Gucy1a3"	Pericytes	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Lymphocyte cells	"Il7r, Rora"	ILC subset 2	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Mast cells	Mcpt4	Mast cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Monocytes	F13a1	Monocytes	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Natural killer (NK) cells	Ccl5	Natural killer (NK) cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Progenitor cells	"Cldn4, AW112010, Tnip3, Mcam"	Damage associated transient progenitors	Tissue	Lung	32750316	Cell Stem Cell	Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration	GSE144468
Mouse	Dendritic cells	"Ccl17, Cxcl16, Siglech"	Dendritic cells	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Stromal cells	"Col1a1, Pdgfra, Pdgfrb"	Adventitial stromal cells	Organoids	Lung	30824323	Immunity	Adventitial Stromal Cells Define Group 2 Innate Lymphoid Cell Tissue Niches	GSE125492
Mouse	Fibroblasts	"Acta2, Ltbp2, Col1a1"	Fibroblasts	Organoids	Lung	30848683	Am J Respir Cell Mol Biol	Defining the Activated Fibroblast Population in Lung Fibrosis Using Single-Cell Sequencing	GSE129605
Mouse	Myofibroblasts	Acta2	Myofibroblasts	Organoids	Lung	30848683	Am J Respir Cell Mol Biol	Defining the Activated Fibroblast Population in Lung Fibrosis Using Single-Cell Sequencing	GSE129605
Mouse	Eosinophils	Prg2	Eosinophils	Tissue	Lung	32213713	JCI Insight	Host immunology and rational immunotherapy for carbapenem-resistant Klebsiella pneumoniae infection	NA
Mouse	Epithelial cells	"EpCAM, Pdpn, Cav1, Ager, Hopx, Aqp5"	ACE1	Tissue	Lung	30913038	JCI Insight	Single-cell RNA sequencing identifies TGF-b as a key regenerative cue following LPS-induced lung injury	GSE113049
Mouse	Basal cells	"Krt5, Trp63, Krt15"	Basal cells	Tissue	Lung	30913038	JCI Insight	Single-cell RNA sequencing identifies TGF-b as a key regenerative cue following LPS-induced lung injury	GSE113049
Mouse	Fibroblasts	Itga8	Fibroblasts	Tissue	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	Hematopoietic cells	"Ptprc, Vav1"	Hematopoietic cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Alveolar cells	"Sftpc, Sftpb, Sftpd"	Alveolar cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Alveolar cells	"Hopx, Pdpn, Ager"	Alveolar cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Fibroblasts	Col1a1	Fibroblasts	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Mesenchymal cells	"Col1a1, Acta2, S100a4;"	Mesenchymal cells	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Neutrophils	"Itpr2, Slc31a2"	Neutrophils	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Monocytes	"Itga4, Ly6c2, Ccr2, Cd62l, Cx3cr1"	Inflammatory monocytes	Tissue	Lung	31744829	Cancer Discov	In Vivo_pigenetic CRISPR Screen Identifies_sf1a_s an Immunotherapeutic Target in_ras-Mutant Lung Adenocarcinoma	NA
Mouse	Lymphocyte cells	"Thy, CD127, KLRG1"	Innate lymphoid cells (ILCs)	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Lymphocyte cells	"Thy, CD127, KLRG1"	Innate lymphoid cells (ILCs)	Tissue	Lung	31353223	Immunity	Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation	NA
Mouse	Macrophages	"Cd68, Mrc1, Lyz2, Adgre1, Axl"	Interstitial marcophages	Tissue	Lung	31601718	Eur Respir J	A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages	NA
Mouse	B cells	"Cd19, Cd79"	B cells	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Monocytes	Cd115	Monocytes	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Natural killer (NK) cells	"Klra4, Klra8"	NK cells	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Lung	31462798	Nature	Metastatic-niche labelling reveals parenchymal cells with stem features	GEO13150
Mouse	Monocytes	"Ly6c2, Ccr2"	Monocytes	Organoids	Lung	31481690	Nat Commun	Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the Mouse lung	GSE94135
Mouse	Leukocytes	Ptprc	Leukocytes	Organoids	Lung	31321669	Sci China Life Sci	Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells	NA
Mouse	Macrophages	"Itgax, Cd206, Retnla, Arg1, Chil3"	Alternatively activated macrophages	Organoids	Lung	32963227	Nat Commun	IL-33-ST2 axis regulates myeloid cell differentiation and activation enabling effective club cell regeneration	GSE155261
Mouse	Macrophages	Siglecf	Alveolar macrophage	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Macrophages	"Ly6c2, Cx3cr1, Cd14, Csf1r, Mrc1, Marco, Itgax, Mrc1"	Alveolar macrophages	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Lung	31604686	Immunity	Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses	GSE102299
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Lung	31604686	Immunity	Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses	GSE102299
Mouse	Macrophages	"Ly6c2, Cx3cr1, Cd14, Csf1r, Mrc1, Csf1r, MHCII"	Interstitial macrophages	Tissue	Lung	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Macrophages	IL-10	Lung interstitial macrophages	Organoids	Lung	31481690	Nat Commun	Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the Mouse lung	GSE94135
Mouse	Macrophages	"MerTK, CD64"	Lung resident macrophages	Tissue	Lung	32220976	Sci Immunol	"Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties"	GSE146682
Mouse	Macrophages	"Itgam, Cd86, Cd80, Ccl2, Il12, Il16"	M1 macrophages	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Macrophages	Nos2	M1-like macrophage cluster 1	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Macrophages	"H2.Aa, H2.Ab1, H2.DMb1, H2.Eb1, Aif1, Tmem176a, Tmem176b, Cd86, Ass1, Cxcl9"	M1 macrophages	Tissue	Lung	31744829	Cancer Discov	In Vivo_pigenetic CRISPR Screen Identifies_sf1a_s an Immunotherapeutic Target in_ras-Mutant Lung Adenocarcinoma	NA
Mouse	Macrophages	CD68	Macrophages	Organoids	Lung	31481690	Nat Commun	Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the Mouse lung	GSE94135
Mouse	Macrophages	"Arg1, Thbs1, Fn1, Cd206"	M2-like macrophages	Tissue	Lung	31744829	Cancer Discov	In Vivo_pigenetic CRISPR Screen Identifies_sf1a_s an Immunotherapeutic Target in_ras-Mutant Lung Adenocarcinoma	NA
Mouse	Macrophages	Mrc1	M2-like tissue macrophage cluster 2	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Macrophages	S100a9	Macrophages	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Macrophages	"Pf4, Cd11b, Aif1, Trem2"	Macrophages	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Macrophages	"Cx3cr1, C1qa, C1qb"	Macrophage I cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Macrophages	"Ccr2, F13a1, Il1b, Il1rn, Lpl, Pparg, Clec7a"	Macrophage II	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Macrophages	"Pparg, Fabp4, Fabp5, Il1rn, Car4, Lpl, Clec7a, Itgax"	Macrophage III	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Macrophages	"Itgax, Siglecf, Cd68, Ccr2"	Macrophages	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Macrophages	"Ccl17, Ccr5, Mafb, C1qb, Cd86, Gpnmb, Spp1, Cd68, Alox15, Saa3, Prg4, Serpinb2, Krt79, Chil3, Car4, Krt19, Marco, Adgre1"	Macrophages	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	B cells	"Cd79a, Cd22, Cd19"	B cells	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Macrophages	"Cd68, Adgre1"	Macrophages	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Natural killer (NK) cells	"Klrb1c, Nkg7"	Natural killer (NK) cells	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Macrophages	"Siglecf, Cd11c"	Alveolar macrophages	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Macrophages	"Ear1, Fabp1"	Alveolar macrophages1	Tissue	Lung	31601718	Eur Respir J	A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages	NA
Mouse	Macrophages	"Car4, Ctsk, Chil3, S100A1, Wfdc21"	Alveolar macrophages2	Tissue	Lung	31601718	Eur Respir J	A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages	NA
Mouse	Macrophages	"Pparg, Car4, Ear1, Siglecf , Marco"	Alveolar macrophages3	Tissue	Lung	31601718	Eur Respir J	A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages	NA
Mouse	Macrophages	"Mrc1, Itgax"	Alveolar marcophages	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	CD4 T cells	"Ccr7, Lef1"	Naive and central memory T cells	Tissue	Lung	31801068	Cell Rep	IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development	GSE139232
Mouse	CD4 T cells	"Junb, Nr4a1"	T cell activation	Tissue	Lung	31801068	Cell Rep	IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development	GSE139232
Mouse	Endothelial cells	"TM4SF1, ENG, ADGRL3, TCF4, EPAS1, CLEC14A, TMEM100, ACER2, LDB2, BMPR2, PLVAP, VWF, CLDN5, CDH5, LRG1, TC2N, AQP1, ABI3BP, RELN, CCL21, PPFIBP1, GNG11, MMRN1, KDR, PRX, CA4, EDNRB, ICAM2, SLCO2A1, KITLG, TMEM47, KIF26B, APLN, FLT1"	Endothelial cells	Organoids	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	Epithelial cells	"DCLK1, SOX9, RGS13, AVIL, POU2F3, LTC4S, SH2D6, PLCG2, SCGB3A1, BPIFB1, TFF3, LYPD2, ALDH1A1, AGR2, SCGB3A2, TPPP3, DNAH9, FAM183A, DNAH11, DYNLRB2, CCDC113, FOXJ1, TMEM212, KRT5, KRT14, KRT15, TP63, S100A2, ABCA3, CXCL17, NPW, SFTPD, S100G, SFTPA1, SFTPB"	Epithelial cells	Organoids	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	Immune cells	"CD3G, CD3E, CD8A, KLRD1, NKG7, S100A8, S100A9, CD68, CD14, TPSB2, IL1RL1, C1QB, PF4, MRC1, NAAA, IL18, GATA3, CCL17, CD86, JCHAIN, CD79A, BANK1, MS4A1, EBF1"	Immune cells	Organoids	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	Mesenchymal cells	"IFITM3, TAGLN, LTBP1, PPP1R14A, DCN, LGALS1, ACTA2, MYH11, TRPC6, PDE5A, ARHGAP42, COX4I2, PDZD2, SOX5, GUCY1A1, UPK1B, NKAIN4, MSLN, IGFBP5, IGFBP6, C4B, GPM6A, COL1A2, COL14A1, GPC3, COL1A1, COL3A1, ELN, MGP, MACF1, GSN, Hsd11b1, COL13A1, FHL1, GPX3, PL"	Mesenchymal cells	Organoids	Lung	31840053	Sci Adv	Single-cell connectomic analysis of adult mammalian lungs	GSE133747
Mouse	B cells	Cd19	B cells	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Lymphocyte cells	Cd3d	Innate lymphoid cells (ILCs)	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Monocytes	S100a9	Monocytes	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Stromal cells	Sparc	Stromal cells	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	Phagocytes	"Cd14, Ctsb, Irf8, Klf4"	Mononuclear phagocytes	Organoids	Lung	31481690	Nat Commun	Non-classical tissue monocytes and two functionally distinct populations of interstitial macrophages populate the Mouse lung	GSE94135
Mouse	Endothelial cells	ICAM2	Endothelial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Epithelial cells	ECAD	Epithelial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Immune cells	CD45	Immune cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Myofibroblasts	SMA	Myofibroblasts	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Endothelial cells	ERG	Nuclear endothelial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Endothelial cells	"Hes1, Flt1"	Stalk endothelial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Endothelial cells	"Esm1, Dll4"	Tip endothelial cells	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Endothelial cells	"Pecam1, Gpihbp1, Plvap, Sox17"	MiEC 1	Tissue	Lung	32091393	eLife	Defining the role of pulmonary Endothelial cells heterogeneity in the response to acute lung injury.	GSE128944
Mouse	Endothelial cells	"Pecam1, Gbp2, Ifi47, Eif3m"	MiEC 2	Tissue	Lung	32091393	eLife	Defining the role of pulmonary Endothelial cells heterogeneity in the response to acute lung injury.	GSE128944
Mouse	Endothelial cells	"Pecam1, Ednrb, Car4, Cd34"	Car4-high ECs	Tissue	Lung	32091393	eLife	Defining the role of pulmonary Endothelial cells heterogeneity in the response to acute lung injury.	GSE128944
Mouse	Endothelial cells	"Pecam1, Hn1, Iigp1, Irf1"	MiEC3	Tissue	Lung	32091393	eLife	Defining the role of pulmonary Endothelial cells heterogeneity in the response to acute lung injury.	GSE128944
Mouse	Endothelial cells	"Pecam1, Lrg1, Vcam1, Vwf"	MaECs	Tissue	Lung	32091393	eLife	Defining the role of pulmonary Endothelial cells heterogeneity in the response to acute lung injury.	GSE128944
Mouse	B cells	"Cd79a, Cd19"	B cells	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Granulocytes	"Il1a, Il1b, Ccl3, Ccl4, Cxcl10"	C13 granulocytes	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Granulocytes	"Cd11b, Ly6g, S100a8, S100a9, IL1b, Csf3r"	C14 granulocytes	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Dendritic cells	"Cd209a, Cd209b, Siglech, Cd300c, Cd74"	Dendritic cells	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Erythrocytes	"Hbb-bs, Hba-a1, Hba-a2"	Erythrocytes	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Lymphocyte cells	NA	Innate lymphoid cells (ILCs)	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Monocytes	"Ccr2, Cd300e, Cd163, Ccl24"	Monocytes	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Myeloid cells	"Ccr2, Ly6C, Cd11b"	Monocytes/macrophages	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	Neutrophils	"Cxcr2, Retnlg"	Neutrophils	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Neutrophils	Retnlg	Neutrophils	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	Neutrophils	"CD45, S100a8, S100a9, Csf3r"	Neutrophils	Cell line	Lung	31591573	Nat Immunol	Locally instructed CXCR4 neutrophils trigger environment-driven allergic asthma through the release of neutrophil extracellular traps.	NA
Mouse	Neutrophils	Ly6G	Neutrophils	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Neutrophils	"S100a9, S100a8, Mmp9, Csf3r, Mmp8, Il1rn, Cxcr2, Ly6g, Itgam, Adgre1, Siglecf, Mpo"	Neutrophils	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Neutrophils	Ly6g	Neutrophils	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Neutrophils	"Cxcr2, S100a9"	Neutrophils	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	B cells	Cd19	B cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Dendritic cells	"Cd86, Itgae"	Dendritic cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Endothelial cells	"Pecam1, Tek"	Endothelial cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Epithelial cells	"Epcam, Cdh1"	Epithelial cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Mesenchymal cells	"Pdgfra, Tcf21, Cdh11"	Mesenchymal cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Natural killer (NK) cells	"Nkg7, Gzmb"	Natural killer (NK) cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	Pericytes	CSPG4	Pericytes	Tissue	Lung	32059772	Dev Cell	Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung	GSE124325
Mouse	Pericytes	Pdgfrb	Pericytes	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Dendritic cells	"Sirpa, S100a4, CD209a"	Non-migratory cDC2s	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Dendritic cells	"Ccr7, Nudt17, Cd81, Gcsam, Laptmb4, Ncoa7"	Migratory cDC1s	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Dendritic cells	"Ccr7, Nudt17, S100a4, Anxa3, Cdc42ep3"	Migratory cDC2s	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Dendritic cells	"Mki67, Stmn1"	Proliferating DC	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Dendritic cells	"Fcgr1, Irf8, Irf4"	Inf-cDC2s	Tissue	Lung	32392463	Immunity	Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection.	GSE149619
Mouse	Endothelial cells	Icam2	Endothelial cells	Organoids	Lung	32414917	Proc Natl Acad Sci U S A	Redundant and additive functions of the four Lef/Tcf transcription factors in lung epithelial progenitors	GSE144170
Mouse	Epithelial cells	Ecad	Epithelial cells	Organoids	Lung	32414917	Proc Natl Acad Sci U S A	Redundant and additive functions of the four Lef/Tcf transcription factors in lung epithelial progenitors	GSE144170
Mouse	Immune cells	Cd45	Immune cells	Organoids	Lung	32414917	Proc Natl Acad Sci U S A	Redundant and additive functions of the four Lef/Tcf transcription factors in lung epithelial progenitors	GSE144170
Mouse	Mesenchymal cells	Ecad	Mesenchymal cells	Organoids	Lung	32414917	Proc Natl Acad Sci U S A	Redundant and additive functions of the four Lef/Tcf transcription factors in lung epithelial progenitors	GSE144170
Mouse	Plasmacytoid dentritic cells	Siglech	Plasmacytoid dentritic cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Airway cells	"Scgb1a1, Foxj1"	Airway cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Alveolar cells	"Rtkn2, Lamp3"	Alveolar cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	B cells	Cd79a	B cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Basal cells	"Krt5, Trp63"	Basal cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Endothelial cells	"Cdh5, Car4, Plvap, Vwf, Prox1"	Endothelial cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Fibroblasts	"Wnt5a, Pdgfra"	Fibroblasts	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	Alveolar cells	"Sftpc, Slc34a2, Scd1, Lamp3, Itih4, Scgb1a1, Cyp2f2, Sftpb"	AT2/club	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	B cells	"Cd79a, Fcmr, Cd79b, Cd19, Fcer2a, Pax5, Cd22"	B cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Dendritic cells	"Clec9a, Cd14, Cd163, Lyz1, Csf1r, Cd300e, Mafb, Batf3, Krt79, Msr1, Itgae, Itgam"	Dendritic cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Fibroblasts	"Pparg, Plin2, Fabp1, Fabp4, Fabp5, Lpl, Lipa, Ear2, Ear1, Mrc1, Ccl6, Plet1, Ctss, Mpeg1, Atp6v0d2, Chil3, Abcg1, Krt79, Cybb, Pdgfra"	Lipofibroblasts	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Fibroblasts	"Col1a1, Col13a1, Col14a1, Fn1, Eln, Vcam1, Fgf10"	Matrix fibroblasts	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Myofibroblasts	"Acta2, Myh11, Tagln, Hhip, Aspn, Mustn1, Enpp2, Igfbp3, Grem2, Lum, Bmp5"	Myofibroblasts	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Natural killer (NK) cells	"Gzma, Klrb1c, Ncr1, Klra4, Eomes, Gzmb, Fasl, Klrk1"	Natural killer (NK) cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Endothelial cells	"Mcam, Pecam1"	Pericytes_endothelial cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	Red cells	Hba-a1	Red blood cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Alveolar cells	"Sftpc, Lyz2"	AT2(alveolar type 2)	Tissue	Lung	32707077	Cancer Cell	Emergence of a High-Plasticity Cell State during Lung Cancer Evolution	GSE152607
Mouse	Alveolar cells	"Hopx, Pdpn"	AT1(normal alveolar type 1)	Tissue	Lung	32707077	Cancer Cell	Emergence of a High-Plasticity Cell State during Lung Cancer Evolution	GSE152607
Mouse	Natural killer (NK) cells	"Ctla2a, Emb, Ccr2, Rps15a, Rpl10a"	Immature Natural killer (NK) cells	Organoids	Lung	32747815	Nat Immunol	ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung	NA
Mouse	Natural killer (NK) cells	"Pim1, Nfkbia, Gadd45b, Ccl4, Icam1"	Natural killer (NK) cells	Organoids	Lung	32747815	Nat Immunol	ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung	NA
Mouse	Natural killer (NK) cells	"Kcnj8, Ly6c2"	Natural killer (NK) cells	Organoids	Lung	32747815	Nat Immunol	ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung	NA
Mouse	Dendritic cells	"Ptprc, Cd3e, Lyz2, Cd19, Itgax"	Dendritic cells	Tissue	Lung	32816604	Autophagy	Autophagic protein ATG5 controls antiviral immunity via glycolytic reprogramming of dendritic cells against respiratory syncytial virus infection	NA
Mouse	Dendritic cells	"Ptprc, Cd3e, Lyz2, Cd19, Itgax"	Dendritic cells	Tissue	Lung	32816604	Autophagy	Autophagic protein ATG5 controls antiviral immunity via glycolytic reprogramming of dendritic cells against respiratory syncytial virus infection	NA
Mouse	B cells	Cd20	B cells	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Lymphocyte cells	Cd3e	T-lymphocytes	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Muscle cells	Acta2	Vascular smooth muscle cells	Tissue	Lung	32855420	Nat Commun	Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages	GSE141733
Mouse	Stromal cells	"Npnt, Col1a1"	Stromal cells	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	T cells	Trbc2	T cells	Tissue	Lung	30318149	Cell	Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting	GSE119228
Mouse	B cells	"Cd79a, Cd79b, Ms4a1, Cd19"	B cells	Organoids	Lung	32977837	Stem Cell Res Ther	Immunosuppressive effects of mesenchymal stem cells on lung B cell gene expression in LPS-induced acute lung injury	NA
Mouse	T cells	"Cd3e, Cd3d"	T cell	Tissue	Lung	31391335	JCI Insight	High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage	GSE133083
Mouse	Epithelial cells	Tm4sf1	Alveolar epithelial progenitors	Tissue	Lung	32989251	Nat Cell Biol	STAT3-BDNF-TrkB signaling promotes alveolar epithelial regeneration after lung injury	GSE132535
Mouse	Lymphocyte cells	"Gata3, Il1rl1"	Innate lymphoid cells (ILCs)	Organoids	Lung	33002412	Immunity	In Situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors	GSE141330
Mouse	Lymphocyte cells	Zbtb16	Innate lymphoid cells progenitors (ILCPs)	Organoids	Lung	33002412	Immunity	In Situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors	GSE141330
Mouse	T cells	Cd3e	T cells	Tissue	Lung	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	T cells	"Cd4, Sell"	C1	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd44, Sell"	C5	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd4, Foxp3"	C6	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd44, Mki67"	C7	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd8a, Sell"	C0	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Cd8a, Sell"	C8	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	Klrg1	C3	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Sell, Gzma, Gzmb"	C10	Tissue	Lung	31883968	Cancer Cell	CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer	GSE129299ï¼_cRNA-seq GSE129299
Mouse	T cells	"Stab1, Cd3, Cd4, CD8, Ifng"	CD4/CD8 T cells	Tissue	Lung	32101596	PLoS Pathog	Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)- driven pulmonary immunopathogenesis	NA
Mouse	T cells	Cd3E	T cells	Tissue	Lung	32317643	Nat Commun	Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis	GSE132771
Mouse	T cells	Cd3e	T cells	Tissue	Lung	32461220	Dis Model Mech	Quantitative single-cell interactomes in normal and virus-infected Mouse lungs	GSE144769
Mouse	T cells	"Cd3d, Cd3e, Cd3g, Cd28, Cd4, Ifng"	T cells	Tissue	Lung	32473656	Cancer Cell	MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate	NA
Mouse	T cells	"Cd3e, Cd68"	T cells	NA	Lung	32581358	Nature	IL-18BP is a secreted immune checkpoint and barrier to IL-18 immunotherapy	GSE146609
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Lung	33116313	Nature	Exuberant fibroblast activity compromises lung function via ADAMTS4	PRJNA612345
Mouse	T cells	Cd3d	T cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Endothelial cells	"Scgb1a1, Foxj1, Sftpc, Hopx"	Endothelial cells	Tissue	Lung	33180746	J Clin Invest	Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium	GSE160876
Mouse	B cells	"Cd19, Tnfrsf17"	Plasma B cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Natural killer (NK) cells	Klrb1c	Natural killer (NK) cells	Tissue	Lung	33357452	Cancer Cell	Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.	GSE158109
Mouse	Lymphocyte cells	"CD3, CD4, CD8a, CD19"	Lymphocytes	Tissue	Lung	33397719	Proc Natl Acad Sci U S A	Single-cell transcriptomic analysis reveals the immune landscape of lung in steroid-resistant asthma exacerbation	NA
Mouse	Myeloid cells	"CD14, CD68, Ly6C"	Monocytes/macrophages	Tissue	Lung	33397719	Proc Natl Acad Sci U S A	Single-cell transcriptomic analysis reveals the immune landscape of lung in steroid-resistant asthma exacerbation	NA
Mouse	Natural killer (NK) cells	NKG7	Natural killer (NK) cells	Tissue	Lung	33397719	Proc Natl Acad Sci U S A	Single-cell transcriptomic analysis reveals the immune landscape of lung in steroid-resistant asthma exacerbation	NA
Mouse	Macrophages	"Ptprc, CD14, Il1b"	Inflammatory macrophages	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Macrophages	"Ptprc, CD14, Mrc1, Cd163"	M2-like macrophages	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Neutrophils	"S100a8, Retnlg"	Neutrophils	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	B cells	"Ptprc, CD19, CD79a"	B cells	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Fibroblasts	"Thy1, Dcn"	Fibroblasts	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Myeloid cells	"Ptprc, CD14"	Myeloid cells	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Myofibroblasts	"Thy1, Dcn, Acta2"	Myofibroblasts	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Natural killer T (NKT) cells	"Ptprc, Thy1, CD3e, Nkg7"	Natural killer T (NKT) cells	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Myeloid cells	"Ptprc, CD14, Mki67"	Proliferating myeloid cells	Tissue	Lung and lymph node	32183351	Cancers (Basel)	"Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo."	NA
Mouse	Capillary phenotype ec 1(capec1)	"Col4a1, Col4a2, Hlx, Id1, Id3, Igfbp3"	Capillary phenotype ec 1(capec1)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Capillary phenotype ec 2(capec2)	"Att3, Cxcl1, Egr1, Fos, Fosb, Jun, Junb, Nfkbia, Nr4a1, Sgk1"	Capillary phenotype ec 2(capec2)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Dark zone	"Ung, Timeless, Cdt1, Mcm2, Mcm3, Mcm4"	Dark zone	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Dark zone proliferating1	"Top2a, Aurkb, Kif11, Prc1, Ndc80, Nusap1, Cdca5, Smc4"	Dark zone proliferating1	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Dark zone proliferating2	"Nek2, Ccnb1, Psrc1, Cdc20, Cenpa, Ccnb2, Cdkn3, Knstrn"	Dark zone proliferating2	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	T cells	"Lag3, Pdcd1, Tnfsf8"	Exhausted T cells	Tissue	Lymph node	31457092	Sci Adv	Aging promotes reorganization ofthe CD4 T cell landscape toward extreme regulatory and effector phenotypes	NA
Mouse	Germinal center	"Cd83, Irf4, Myc, Nfkbia, Cxcr4, Bcl6, Foxo1, Bach2, Aicda, Akt1, Bcl2l11, Cd86, Ezh2, Fos, Mki67, Rela"	Germinal center	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Interferon-stimulated gene-enriched capec (capifn)	"Cxcl9, Cxcl10, Irf7, Isg15, Lgals9"	Interferon-stimulated gene-enriched capec (capifn)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Interfollicular reticular cells	Ch25h	Interfollicular reticular cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Light zone	"Cd86, Syk, Cd79b, Cxcr5, Cd19, Icosl, Bank1, Cd83, Il4ra, Cd74"	Light zone	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Light zone selected	"Mif, Pa2g4, Nolc1, Nhp2, Fbl, Npm1, Gnl3, Hspe1, Ldha, Mrto4"	Light zone selected	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Lymphatic valve	Foxc2	Lymphatic valve	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Marginal reticular cells	"Cr2, Madcam1, Mfge8, Tnfsf11, Ch25h, Hamp"	Marginal reticular cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Medullary reticular cells	Lum	Medullary reticular cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Naive cells	"Lef1, Sell, Igfbp4"	Naive cells	Tissue	Lymph node	31457092	Sci Adv	Aging promotes reorganization ofthe CD4 T cell landscape toward extreme regulatory and effector phenotypes	NA
Mouse	Non-hec veins (vn)	"Ackr1, Icam1, Nr2f2, Sele, Selp, Vcam1, Vwf"	Non-hec veins (vn)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Peripheral capillary lymphatic vessels	"Ccl21, Lyve1"	Peripheral capillary lymphatic vessels	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Peripheral lymphatic vessels	"Lyve1, Ccl21"	Peripheral lymphatic vessels	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Reticulocytes	Cd21	Reticulocytes	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Endothelial cells	Stab2	Sinusoidal endothelial	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Subcapsular sinus ceiling	Ackr4	Subcapsular sinus ceiling	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Subcapsular sinus floor	Madcam1	Subcapsular sinus floor	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	T_b border reticular cells	"Ccl21a, Ccl19, Fmod"	T_b border reticular cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Transitional ec (trec)	"Apoe, St3gal6"	Transitional ec (trec)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Valve	"Cldn11, Esam, Foxc2, Gata2"	Valve	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Progenitor cells	"Angpt2, Apln, Esm1, Mcam, Nid2, Pdgfb, Pgf, Vim"	Capillary resident progenitors	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	T cells	"Gzmk, Eomes, Ctla2a"	Cytotoxic T cells	Tissue	Lymph node	31457092	Sci Adv	Aging promotes reorganization ofthe CD4 T cell landscape toward extreme regulatory and effector phenotypes	NA
Mouse	T cells	"Lgals1, S100a4, Itgb1"	Effector memory T cells	Tissue	Lymph node	31457092	Sci Adv	Aging promotes reorganization ofthe CD4 T cell landscape toward extreme regulatory and effector phenotypes	NA
Mouse	Plasma cells	"Jchain, Mzb1, Os9, Derl3, Edem2, Prdm1, Irf4, Cxcr3, Tnfrsf17"	Plasma cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Plasmablasts	"Cd79a, Cd79b, Xbp1, Sdc1, Fkbp11, Mki67, Top2a, Cdk1, Ccna2, Cdca3"	Plasmablasts	Tissue	Lymph node	32591393	J IMMUNOL	A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection	GSE149036
Mouse	Dendritic cells	"Cxcl1, Cxcl16, Il6, Gstp1, Ptgs2, Cd151, Clec14a, Plat, Ptn, Ecm1, Mmp3, Mmp9, FcεR2A, CD21, CD35, TdTom, MYH11, PDLIM3, Pdlim3"	Dark zone follicular dendritic cells (FDC2)	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Dendritic cells	"Cr2, Madcam1, Mfge8"	Follicular dendritic cells	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	Dendritic cells	"Cr2, Fcamr, Fcer2a, Fcgr2b, Coch, Homer2, Postn, Tmem119, Myh11, Sncg, FcεR2A, CD21, CD35, TdTom, MYH11"	Light zone follicular dendritic cells (FDC1)	Tissue	Lymph node	32424359	Nat Immunol	Remodeling of light and dark zone follicular dendritic cells governs germinal center responses	"E-MTAB-8445, E-MTAB-8454, E-MTAB-8904"
Mouse	B cells	B220	B cells	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	"Ackr4, Cav1, Bmp4, Cd93, Cldn5, Jag1, Pdgfa, Pdgfb, Stab2, Cd9, Cdh13, Edn1, Fabp4, Fn1, Gdf10, Gja4, Klf4, Mmrn1, Mmrn2, Nts, Nudt4"	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	"Ccl20, Bmp2, Lyve1, Madcam1, Pd-l1, Cd274, Bmp2, Cd74, C2, Clu, Csf1, Ifngr2, Il33, Ltb, Mmp9, Relb, Vcam1, Msr1, Cxcl1, Cxcl16, Glycam1, H2-Ab1, Icam1, Pf4, Smad1, Smad4, Vcam1"	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	"C2, Cd274, Clec4g, Csf1, Csf2rb, F8, Il2rg, Il33, Ltbp2, Marco, Tnc, Tspan7, Clec1b, Kdr, Lyve1"	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	Prox1	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	"Reln, Angpt2, Stab2, Tgfbi, Ccl21a, Flt4, Itih5, Kdr, Lyve1, Mgll, Mrc1, Npr1, Npr2, Ptx3"	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	Endothelial cells	Ptn	Lymphatic endothelial cells (LECs)	Tissue	Lymph node	32426372	Front Cardiovasc Med	A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature	"GSE143877, GSE145121"
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Lymph node	30936494	Nature Immunology	Adaptive plasticity of IL-10 and IL-35 T cells cooperatively promotes tumor T cell exhaustion.	GSE126184.
Mouse	T cells	"Foxp3, Il2ra, Ikzf2"	Regulatory T cells (Treg)	Tissue	Lymph node	31457092	Sci Adv	Aging promotes reorganization ofthe CD4 T cell landscape toward extreme regulatory and effector phenotypes	NA
Mouse	Arterial ec	"Bmx, Depp1, Gja4, Gja5, Gkn3, Sox17"	Arterial ec (pre-art)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	Endothelial cells	"Ccl21a, Chst4, Glycam1"	High endothelial cells (HEC)	Tissue	Lymph node	32732867	Nat Commun	A molecular map of murine lymph node blood vascular endothelium at single cell resolution	GSE140348
Mouse	T cells	"Cd8b1, Ms4a4b, Cd3d, Cd3e, Ccr7, Il7r"	T cells	Tissue	Lymph node	32591393	J IMMUNOL	A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection	GSE149036
Mouse	Mesoderm cells	"Lhx2, Tnnt1"	Head mesoderm cells.	Tissue	Mandibular arch	30638444	eLife	Hedgehog signaling patterns the oral-aboral axis of the mandibular arch.	GSE112837
Mouse	Mesenchymal cells	Barx1	Neural crest derived mesenchyme cells 1	Tissue	Mandibular arch	30638444	eLife	Hedgehog signaling patterns the oral-aboral axis of the mandibular arch.	GSE112837
Mouse	Mesenchymal cells	Hand2	Neural crest derived mesenchyme cells 2	Tissue	Mandibular arch	30638444	eLife	Hedgehog signaling patterns the oral-aboral axis of the mandibular arch.	GSE112837
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Mandibular arch	30638444	eLife	Hedgehog signaling patterns the oral-aboral axis of the mandibular arch.	GSE112837
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Mandibular arch	30638444	eLife	Hedgehog signaling patterns the oral-aboral axis of the mandibular arch.	GSE112837
Mouse	Hematopoietic cells	"Prtn3, Lmo2, Cdk6, Cd34, Ms4a3"	Hematopoietic stem and progenitor cells	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	T cells	"Cd3d , Trbc2"	T cells	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	B cells	"Cd79a, Ebf1, Iglc2, H2-Aa, H2-Eb1"	B Lymphocytes	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	B cells	"Cd79a, Ebf1, Mzb1, Vpreb3"	"Pro-B, Pre-B"	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	Dendritic cells	"Tcf4, Ccr9, Siglech"	Dendritic cells	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	Monocytes	"Fn1, Ctss"	Monocytes	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	Natural killer (NK) cells	"Klrd1, Klrk1, Klre1, Gzma"	Natural killer (NK) cells	Tissue	Marrow	33154494	Sci Rep	The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution.	GSE148115
Mouse	Proliferating cells	Ki67	Proliferative cells	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Tumor cells	"Dct, MITF, Pmel"	Melanocytes	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Tumor cells	"S100b, MCAM , Sox10"	Melanoma	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Mesenchymal cells	Pdgfra	Mesenchymal cells	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Neural cells	"Nestin, Tubb3 , Ngfr"	Neural crest cells	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Neural cells	"Foxd3, L1cam"	Neural crest cells	Tissue	Melanoma	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Adipocytes	Pdgfra	Adipose mesenchymal cells and precursors	Tissue	Mesentery	29728440	J Exp Med	Peripheral PDGFRalphagp38 mesenchymal cells support the differentiation of fetal liver-derived ILC2.	GSE102665
Mouse	Lymphocyte cells	KLRG1	ILC2/NK	Tissue	Mesentery	29728440	J Exp Med	Peripheral PDGFRalphagp38 mesenchymal cells support the differentiation of fetal liver-derived ILC2.	GSE102665
Mouse	M cells	"Zmat3, Mmp15, Myadm, Anxa5, Marcksl1"	M cells	Organoids	Mini-intestine	32939089	Nature	Homeostatic mini-intestines through scaffold-guided organoid morphogenesis	NA
Mouse	Regenerating cells	Ly6a	Regenerating cells	Organoids	Mini-intestine	32939089	Nature	Homeostatic mini-intestines through scaffold-guided organoid morphogenesis	NA
Mouse	Stem cells	"Clu, Msln"	Revival stem cells	Organoids	Mini-intestine	32939089	Nature	Homeostatic mini-intestines through scaffold-guided organoid morphogenesis	NA
Mouse	Enterocytes	"Fgfbp1, Dmbt1, Pdss1, Prss32"	Immature enterocytes	Organoids	Mini-intestine	32939089	Nature	Homeostatic mini-intestines through scaffold-guided organoid morphogenesis	NA
Mouse	Enterocytes	"Ada, Ifrd1, Krt20, Pmp22, Serpinb1a"	Villus-top enterocytes	Organoids	Mini-intestine	32939089	Nature	Homeostatic mini-intestines through scaffold-guided organoid morphogenesis	NA
Mouse	Mesenchymal cells	"Fgfr3, Postn"	Cluster 0	Tissue	Molars	33038290	Stem Cells	Stem cell contributions to cementoblast differentiation in healthy periodontal ligament and periodontitis	NA
Mouse	Mesenchymal cells	"Dmp1, Ibsp, Bglap"	Cluster 2	Tissue	Molars	33038290	Stem Cells	Stem cell contributions to cementoblast differentiation in healthy periodontal ligament and periodontitis	NA
Mouse	Mesenchymal cells	"Apod, Ccl11"	Cluster 3	Tissue	Molars	33038290	Stem Cells	Stem cell contributions to cementoblast differentiation in healthy periodontal ligament and periodontitis	NA
Mouse	Gabaergic acs	"Gad1, Gad2"	Gabaergic acs	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Glycinergic acs	"Slc6a5, Slc6a9"	Glycinergic acs	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Primary prcs	"Ccnd2, Fgf15"	Primary prcs	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Reticulocytes	"Hba-a1, Hba-a2, Hbb-bs, Hbb-bt"	Reticulocytes	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Ganglion cells	"Isl2, Pou4f1, Pou4f2, Pou4f3, Rbpms"	Retinal ganglion cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Epithelial cell	"Lrat, Pmel, Rpe65, Tyr"	Retina pigment epithelium	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Rods	"Guca1b, Nrl, Rho, Rom1"	Rods	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Bipolar cells	"Bhlhe23, Cabp5"	Bipolar cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Cones	"Arr3, Cnga3, Opn1mw, Opn1sw, Thrb"	Cones	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Horizontal cells	"Lhx1, Onecut1, Onecut2"	Horizontal cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Astrocytes	Gfap	Astrocytes	Cell line	Muller glia	31383796	Development	"MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Mu_ ller glia in Mouse"	GSE135816
Mouse	Endothelial cells	Fn1	Endothelial cells	Cell line	Muller glia	31383796	Development	"MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Mu_ ller glia in Mouse"	GSE135816
Mouse	Microglia cells	Aif1	Microglia cells	Cell line	Muller glia	31383796	Development	"MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Mu_ ller glia in Mouse"	GSE135816
Mouse	Neural cells	Prox1	Neurons	Cell line	Muller glia	31383796	Development	"MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Mu_ ller glia in Mouse"	GSE135816
Mouse	Muller cells	"Abca8a, Aldh1a1, Kcnj10"	Muller cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Muller cells	"Aqu4, Rlbp1, Glul, Cnnd1, GLAST, Slc1a3"	Muller glia cells	Cell line	Muller glia	31383796	Development	"MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Mu_ ller glia in Mouse"	GSE135816
Mouse	Pericytes	"Acta2, Kcnj8, Pdgfrb"	Pericytes	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Progenitor cells	Cdk4	Retinal progenitor cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Amacrine cells	"Cbln4, Tfap2b"	Amacrine cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Astrocytes	"Pax2, Pdgfra, S100b"	Astrocytes	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Microglia cells	"Csf2rb, Csf2rb2, Cx3cr1, Mpeg1, Ptprc, Tmem119"	Microglia cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Oligodendrocytes	"Mbp, Mog, Olig1"	Oligodendrocytes	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	Endothelial cells	"Cdh5, Pecam1, Tek, Tie1"	Vascular/endothelial cells	Tissue	Muller glia	33004674	Science	Gene regulatory networks controlling vertebrate retinal regeneration	GSE135406
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Tbx1"	Pharynx	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Nkx2-1, Foxa2"	Respiratory	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Sox2"	Esophagus	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Sox2, Osr1"	Stomach	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Alb, Prox1, Afp"	Hepatic	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Sox17, Pdx1"	Ventral hepatopancreatic duct	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Mnx1, Pdx1"	Dorsal pancreas	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	De cluster	"Foxa1, Foxa2, Cdh1, Epcam, Cdx2"	Duodenum	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Distal tubule cells	"Slc12a1, Spp2, Lrp2, Wfdc15b, Ppp1r1a, kng2, Umod, Atp1a1"	Distal tubule cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Dividing cells	"Stmn1, Top2a, Mki67, Hmgb2, Tubb5, Cks1b, Plac8, Pclaf"	Dividing cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Intercalated cells	"Slc12a1, Atp6v1g3, Hsd11b2, Aqp4, Aqp2, Spp2, Lrp2"	Intercalated cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Intercalated cells	"Atp6v1g3, Tfcp2l1, Atp6v0d2, Tmeme213, Car2"	Intercalated cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Melanoma cells	CD31	Intravascular melanoma cells	Tissue	Multiple tissues	32553158	Cell Rep	Human metastaticmelanoma patient GSE72056Single Cell RNaseq data from NRAS Mouse model GEO	GSE148666
Mouse	Loop of henle	"Aqp1, Spp2, Lrp2, Cryab, Apela, Bst1, Epcam, Plet1"	Loop of henle	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Mp	"Sell, Cd28, Il7r, Cd27, Cxcr3"	Mp	Tissue	Multiple tissues	32728699	J Exp Med	A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool.	GSE152282
Mouse	NA	"Tcf1, Slamf6"	TM cells	Tissue	Multiple tissues	32846135	Cell Rep	Landscape of Exhausted Virus-Specific CD8 T Cells in Chronic LCMV Infection	PRJEB36998
Mouse	NA	Cx3cr1	TE cells	Tissue	Multiple tissues	32846135	Cell Rep	Landscape of Exhausted Virus-Specific CD8 T Cells in Chronic LCMV Infection	PRJEB36998
Mouse	Principal cells	"Hsd11b2, Aqp4, Aqp2, Spp2, Lrp2, Aqp3, Fxyd4, Rhcg"	Principal cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Sm	"Foxf1, Vim, Pdgfra, Tbx1, Prrx1"	Pharyngeal	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Cardiac cells	"Foxf1, Vim, Pdgfra, Isl1, Mtus2"	Cardiac outflow tract cells	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Sm	"Foxf1, Vim, Pdgfra, Nkx6-1, Gata4, Wnt2"	Respiratory	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Sm	"Foxf1, Vim, Pdgfra, Nkx6-1, Sfrp2, Wnt4"	Esophageal mesenchyme	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Sm	"Foxf1, Vim, Pdgfra, Barx1, Hlx"	Stomach mesenchyme populations	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Sm	"Foxf1, Vim, Pdgfra, Hand1, Hoxc8"	Duodenum mesenchyme population	Tissue	Multiple tissues	32855417	Nat Commun	Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis	"GSE136689, GSE136687"
Mouse	Te	"Klf2, Tbx21, Cx3cr1, Klrg1, Zeb2"	Te	Tissue	Multiple tissues	32728699	J Exp Med	A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool.	GSE152282
Mouse	Tip cells	"Apln, Col4a2, Trp53i11"	Tip cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Tissue-resident memory T cells	"CD103, CD69"	Tissue-resident memory T cells	Tissue	Multiple tissues	32728699	J Exp Med	A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool.	GSE152282
Mouse	CD8 T cells	"CD8, Il7r, Cxcr3"	MEMORY	Tissue	Multiple tissues	29326266	Science	The epigenetic control of stemness in CD8 + T cell fate commitment	"GSE106264, GSE106265, GSE106267"
Mouse	CD8 T cells	"CD8, Klrg1, Zeb2"	EFFECTOR	Tissue	Multiple tissues	29326266	Science	The epigenetic control of stemness in CD8 + T cell fate commitment	"GSE106264, GSE106265, GSE106267"
Mouse	CD8 T cells	"CD8, Mcm5, Pcna"	CYCLING	Tissue	Multiple tissues	29326266	Science	The epigenetic control of stemness in CD8 + T cell fate commitment	"GSE106264, GSE106265, GSE106267"
Mouse	CD8 T cells	"CD8, Cxcr6, Rnf138, ll18r1, Traf1"	STEMNESS	Tissue	Multiple tissues	29326266	Science	The epigenetic control of stemness in CD8 + T cell fate commitment	"GSE106264, GSE106265, GSE106267"
Mouse	B cells	"Clec4F, RFP"	B cells	Tissue	Multiple tissues	30076102	Immunity	The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages	GSE117081
Mouse	T cells	"CD69, CD103, CD127"	Effector T cells	Tissue	Multiple tissues	32728699	J Exp Med	A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool.	GSE152282
Mouse	T cells	"Gzmb, Ifng, Tbx21, Klra1, Klra7, Klra9"	Cluster2 and 4	Tissue	Multiple tissues	31257026	Cell	Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors	GSE123508
Mouse	Endothelial cells	"CD31, CENPE, EOMES, GLAST, TOP2A"	C6	Tissue	Multiple tissues	31091443	Cell Rep	Mesenchymal Stromal Cells Are Required for Regeneration and Homeostatic Maintenance of Skeletal Muscle	NA
Mouse	Hepatic stellate cells	"Dcn, Aebp1, Timp2, C3, Serping1, C1s1, Col1a2"	Hepatic stellate cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Kupffer cells	"Cd5l, C1qc, Csf1r, Ctsc, Ctss, Clec4f, Vsig4, Laptm5, Cd44, C1qa, Ptprc, Lyz2, Adgre1, C1qb"	Kupffer cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Leukocytes	Ptprc	Leukocytes	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Macrophages	Zeb2	Macrophages	Tissue	Multiple tissues	30076102	Immunity	The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages	GSE117081
Mouse	Dendritic cells	"MhcII, Cd11c, XCR1, CLEC9A, CD8A, IRF8"	CLEC9A+XCR1+cDC1	NA	Multiple tissues	31668803	Cell	Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity	GSE137710
Mouse	Dendritic cells	"MhcII, Cd11c, DTX1, ESAM"	T-bet+CD11b+SIRPa+cDC2	NA	Multiple tissues	31668803	Cell	Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity	GSE137710
Mouse	Dendritic cells	"MhcII, Cd11c, CLEC12A, CX3CR1, CD14, IL1A, P2RX7, CLEC10A, NKG2D, MGL2, CD209A"	T-bet-CD11b+SIRPa+cDC2	NA	Multiple tissues	31668803	Cell	Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity	GSE137710
Mouse	Monocytes	Ly6C	Monocytes	NA	Multiple tissues	31668803	Cell	Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity	GSE137710
Mouse	Macrophages	"Ccl9, Lgals3, Arg1, Lyz2, Ccl6, Ctss, Mpeg1, Cybb"	Macrophages	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Mait-like cells	"Cxcr6, Rorc, Icos, Zbtb16, Tmem176a, ll17a, Rorc"	Mait-like cells	Tissue	Multiple tissues	31257026	Cell	Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors	GSE123508
Mouse	Endothelial cells	"Slc2a1, Itm2a, Bsg, Slcolc1, Pglyrp1"	Brain endothelial cells	Tissue	Multiple tissues	31850371	Front Cardiovasc Med	Single Cell Analysis of Endothelial cellss Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features	"GSE122403, GSE109774"
Mouse	Endothelial cells	"Clec4g, Dnase113"	Liver Endothelial cells	Tissue	Multiple tissues	31850371	Front Cardiovasc Med	Single Cell Analysis of Endothelial cellss Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features	"GSE122403, GSE109774"
Mouse	Endothelial cells	"Tmem100, Foxf1a, Ace"	Lung	Tissue	Multiple tissues	31850371	Front Cardiovasc Med	Single Cell Analysis of Endothelial cellss Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features	"GSE122403, GSE109774"
Mouse	Endothelial cells	"Csf2rb, Angptl4"	Fat endothelial cells	Tissue	Multiple tissues	31850371	Front Cardiovasc Med	Single Cell Analysis of Endothelial cellss Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features	"GSE122403, GSE109774"
Mouse	Endothelial cells	Slc28a2	Heart endothelial cells	Tissue	Multiple tissues	31850371	Front Cardiovasc Med	Single Cell Analysis of Endothelial cellss Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features	"GSE122403, GSE109774"
Mouse	Endothelial cells	"Cd31, Cdh5"	Endothelial cells	Tissue	Multiple tissues	31944177	eLife	"Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells"	"GSE99235, GSE98816"
Mouse	Endothelial cells	"Gkn3, Hey1"	Brain arterial endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	Esm1	Choroid plexus capillary endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	"Cdh5, Pecam1"	Endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Fibroblasts	Col1a1	Fibroblasts	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	"Fbln5, Hey1, Mecom, Cxcl12, Rbp7, Kdr, Endou, Vcam1, Fmo1, Fmo2, Mgp, Cfh, Bgn, Vwf, Isg15, lfit1, lfit3, lfit3b, Rgcc, Trp53i11, Col4a1, Lgals1, Aplnr, Apln"	Heart endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	"Prox1, Lyve-1.Pdpn"	Lymphatic endothelial cells (LECs)	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Muscle cells	Acta2	Smooth muscle cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	"Pecam1, Cdh5"	Vascular endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Endothelial cells	Bgn	Venous endothelial cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Neutrophils	"S100a9, S100a8, Lilr4b, Tyrobp, Cebpb, S100a11"	Neutrophils	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Pericytes	Pdgfrb	Pericytes	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	Phagocytes	NA	Fibroblasts and mononuclear phagocytes	Tissue	Multiple tissues	30356220	Nature	Gene expression variability across cells and species shapes innate immunity	"E-MTAB-5918, E-MTAB-5919, E-MTAB-5920, E-MTAB-6754, E-MTAB-6773, E-MTAB-5988, E-MTAB-5989, E-MTAB-6831, E-MTAB-6066, E-MTAB-7032, E-MTAB-7037, E-MTAB-7051, E-MTAB-7052."
Mouse	Plasma cells	"Mzb1, Igkc, Jchain, H13, Txndc5, Sec11c, Herpud1"	Plasma cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Proximal tubular cells	"Spp2, Lrp2, Slc34a1, Miox, Acsm2, Acsm2, Acsm2"	Proximal tubular cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Red cells	"Hba-a1, Hbaa2, Hbb-bs"	Red blood cells	Tissue	Multiple tissues	32059779	Cell	Single-Cell Transcriptome Atlas of Murine Endothelial cellss	GSE99235
Mouse	B cells	"Cd79a, Cd19, Cd79b"	B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	B cells	"CD21, CD23"	B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	B cells	NA	B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	B cells	"CD5, IgM"	CD11B B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	B cells	"IgM, IgD, CD21, CD23."	CD11B- B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	Endothelial cells	CD31	Endothelial cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	B cells	"Nr4a1, Junb, Fos, Dusp1, Ppp1r15a, Sertad1, Plaur, Vps37b, Ier2, H3f3b, Plk2, Cebpb, Ubc, Hspa5, Pnrc1, Eif1, Litaf, Hspa8, Tuba1c, Rrad, Hs3st1, Blk, Samhd1, mt-Nd5, Foxp1, Arpc5l, Tcf3, Ikzf3, Gm30211, Ifi27l2a, Arhgap45, Pld4, Hck, mt-Atp8, Pou2f2, mt-"	Organ-associated B cells	Organoids	Multiple tissues	32663200	JCI Insight	Developmental changes in myocardial B cells mirror changes in B cells associated with different organs	GSE153569
Mouse	Antigen-presenting cells (APC)	"Psap, Fcer1g, Cd74"	Antigen-presenting cells (APC)	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Artery and vein	"Kdr, Cdh5, Aqp1, Spp2, Lrp2, lfitm3, Ly6c1, H2-D1, Emcn"	Artery and vein	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	B cells	"Cd79a, Ighm, Cd74, Ebf1, Igkc, H2-Aa, H2-Eb1, Ebf1"	B cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Dendritic cells	"Laptm5, Coro1a, Sh3bgrl3, Alox5ap, Spi1, Lsp1, Cd74, Gm2a, Syngr2"	Dendritic cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Endothelial cells	"Aqp1, Dnase1l3, Igfbp7, Gpr182, Ptprb, Eng, Kdr, Ehd3, Oit3, Fcgr2b, Mcam"	Liver sinusoidal Endothelial cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Endothelial cells	"Rspo3, Wnt2, Adgrg6, Efnb1, Gpr182, Ptprb, Aqp1, Adgrf5, Gpihbp1, Eng, Dnase1l3, Igfbp7"	Endothelial cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Endothelial cells	"Rspo3, Wnt2"	Endo-pc	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Endothelial cells	"Adgrg6, Efnb1"	Endo-pp	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Muscle cells	"Spp2, Lrp2, Cnn1, Myl9, Acta2, Tagln, Sparcl1, Mylk"	Vascular smooth muscle cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	T cells	"Ptprc, Nkg7, Ccl5, Tmsb10, Vps37b, Il2rb, Ptpn22, Trbc2"	T cells	Organoids	Multiple tissues	32949498	Cell Metab	Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 high Cells In Vivo	GSE155182
Mouse	Ec	"Pecam1, Kdr"	Ec	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Ec	Pecam-1	Ec	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Faps	Pdgfra	Faps	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Faps	Pdgfra	Faps	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Muscle cells	Acta1	Mature skeletal muscle	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Mph	Adgre1	Mph	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Myh1"	IIx	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Myh4"	IIb	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Myh2"	IIa	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Myh1, Myh4, Tnnc2, Tnni2, Mb, Cox6a2, Cox6c, Atp5e, Atp5g1"	IIx_b	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Chrne, Colq, Prkar1a, Col25a1, Lama2"	NMJ	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonuclei	"Ckm, Col22a1, Lama2"	MTJ	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myonucler	"Tnnc2, Myh4"	Myonucler	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Pro-inflammatory maccrophages	Ccl6	Pro-inflammatory maccrophages	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Prolif ic	"Mik67, Top2a"	Prolif ic	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Regmyon	"Myh3, Myh8"	Regmyon	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Stem cells	"Vcam1, Myod1, Myf5, Des"	Skeletal muscle stem cells	Tissue	Muscle	30890574	DEVELOPMENT	Single cell analysis of adult Mouse skeletal muscle stem cells in homeostatic and regenerative conditions	NA
Mouse	Stem cells	VCAM1	Skeletal muscle stem cells	Tissue	Muscle	30890574	DEVELOPMENT	Single cell analysis of adult Mouse skeletal muscle stem cells in homeostatic and regenerative conditions	NA
Mouse	Tc	Mkx	Tc	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Tenocytes	Scx	Tenocytes	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Tenocytes	"Scx, Tnmd"	Tenocytes	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Progenitor cells	"Prrx1, Col1a1"	Fibro-adipogenic progenitors	Tissue	Muscle	32533926	Am J Pathol	Myocardial B cells are a subset of circulating lymphocytes with delayed transit through the heart	GSE144270
Mouse	Progenitor cells	Pdgfra	Fifibro/adipogenic progenitors	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Glial cells	Ptn	Glial cells	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Macrophages	C1qa	Anti-inflammatory macrophages	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Macrophages	Cxcl3	M1 macrophages	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Macrophages	Cxcl3	M2 macrophages	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Macrophages	Cd74	Resident macrophage	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Muscle cells	Pax7	Muscle stem cells	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Muscle cells	"Pax7, Myod1"	Muscle stem cells	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Muscle cells	Pax7	Muscle stem cells	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Myoblasts	Megf10	Myoblasts	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Neutrophils	"S100a8, Cxcl3, S100a9"	Neutrophils	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Muscle cells	Myl9	Smooth muscle cells	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	Antigen-presenting cells (APC)	Ccr7	Antigen-presenting cells (APC)	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Fibroblasts	"Col3a1, Ly6a, Col1aa"	Fibroblasts	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Monocytes	Acp5	Monocytes	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Pericytes	"Notch3, Rgs5"	Pericytes	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Schwann cells	Mpz	Schwann cells	Tissue	Muscle	32160558	Cell Rep	Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration	"GSE143435, GSE143437"
Mouse	T cells	Loxl2	Angiogenic S1 cells	Tissue	Muscle	32226549	Theranostics	CD8 + T-cell plasticity regulates vascular regeneration in type-2 diabetes	PRJNA593898
Mouse	T cells	"Ccr7, Sell"	Central memory S1 cells	Tissue	Muscle	32226549	Theranostics	CD8 + T-cell plasticity regulates vascular regeneration in type-2 diabetes	PRJNA593898
Mouse	T cells	"Klrg1, Cd44, Ifngr1, Stat4, Zeb2, Id2h"	Effector S2 cells	Tissue	Muscle	32226549	Theranostics	CD8 + T-cell plasticity regulates vascular regeneration in type-2 diabetes	PRJNA593898
Mouse	T cells	"Cd28, Id2"	Effector memory S2 cells	Tissue	Muscle	32226549	Theranostics	CD8 + T-cell plasticity regulates vascular regeneration in type-2 diabetes	PRJNA593898
Mouse	T cells	"Id3, Cd69"	Tissue resident memory S3 cells	Tissue	Muscle	32226549	Theranostics	CD8 + T-cell plasticity regulates vascular regeneration in type-2 diabetes	PRJNA593898
Mouse	T cells	Ccr7	T cells	Tissue	Muscle	32248062	iScience	Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.	GSE138826
Mouse	Muscle cells	Myh11	Smooth muscle cells	Tissue	Muscle	33148801	Proc Natl Acad Sci U S A	Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing	GSE156498
Mouse	Caps	Fap	Caps	Tissue	NA	33298926	Nat commun	TGFbeta-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	GSE160687
Mouse	Cluster5	Cd24a	Cluster5	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Cluster5	Cd24a	Cluster5	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Dn2 cells	"Cd117, Cd44, Hoxa9, Lmo2, Mef2c, Gfi1b, Lyl1, Spi1, Bcl11a, Mycn, Hhex"	Dn2 cells	NA	NA	30765463	J Exp Med	The transcription factor Duxbl mediates elimination of pre-T cells that fail beta-selection	GSE118059
Mouse	Dn3 cells	"CD3gamma, CD3delta, CD3ε, Rag1, Rag2, Ptcra, Tcf12, Ets, Ahr, Notch3, SpiB"	Dn3 cells	NA	NA	30765463	J Exp Med	The transcription factor Duxbl mediates elimination of pre-T cells that fail beta-selection	GSE118059
Mouse	Dn4 cells	"Cd4, Cd8, Rorc, Id3"	Dn4 cells	NA	NA	30765463	J Exp Med	The transcription factor Duxbl mediates elimination of pre-T cells that fail beta-selection	GSE118059
Mouse	Mature classical dc	"Syngr2, Cd83, Fscn1, Cacnb3, Ccr7, Ccl22"	Mature classical dc	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Mg	Glul	Mg	Tissue	NA	32075759	Cell Rep	STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina	NA
Mouse	Mg	Glul	Mg	Tissue	NA	32075759	Cell Rep	STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina	NA
Mouse	Monocytes	"Itgam, Ms4a4c, Oasl1, Cxcl10, Isg15, Rsad2, Ifit1, Ifit2, Ifit3"	Monocyte-derived ifn-induced cells	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Myeloid cells	S100a9	Myeloid-derived suppressor cells (mdsc)	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Myeloid cells	"Itgam, Arg1, Spp1, Fn1, Clec4d, Prdx1"	Myeloid-derived suppressor cells (mdsc)	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Proliferating cells	Mki67	Proliferating cells	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Seminal vesicle	"Pax2, Pate4, Calml3"	Seminal vesicle	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Spermatocytes	"Plzf, Sall4, Vasa"	Spermatogonia and germ cell	Tissue	NA	30026551	Nat Commun	Identification of dynamic undifferentiated cell states within the male germline	GSE107256
Mouse	Spg1	"Id4, Etv5, Gfra1, Lhx1, Ret"	Spg1	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117708
Mouse	Spg1	"Id4, Etv5, Gfra1, Lhx1, Ret"	Spg1	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117708
Mouse	Spg2	"Ddit4, Utf1, Egr4, Pramef12, Sall4, Plzf"	Spg2	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117709
Mouse	Spg2	"Ddit4, Utf1, Egr4, Pramef12, Sall4, Plzf"	Spg2	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117709
Mouse	Spg3	"Kit, Sra8 , Dnmt3b, Pramef12, Sall4, Plzf"	Spg3	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117710
Mouse	Spg3	"Kit, Sra8 , Dnmt3b, Pramef12, Sall4, Plzf"	Spg3	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117710
Mouse	Spg4	"Prss50, Ly6k, Hormad1, Prdm9"	Spg4	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117711
Mouse	Spg4	"Prss50, Ly6k, Hormad1, Prdm9"	Spg4	Tissue	NA	31729367	Nat Commun	Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in Mouse	GSE117711
Mouse	"Tam, m1-like"	"Itgam, Adgre1, C1qc, Sepp1, Cxcl9, Cxcl10, Ccl2, Ccl12"	"Tam, m1-like"	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m1-proliferating"	"Itgam, Adgre1, C1qc, Cx3cr1, Ccl2, Stmm1, Hmyb2, Top2a, Mki67, Cd3g, Cd8a, Slamf6"	Stem CD8+ T	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m2a-like"	"Itgam, Adgre1, C1qc, Ctsd, Arg1, Hmox1, Mmp12"	"Tam, m2a-like"	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m2b-like"	"Itgam, Adgre1, C1qc, Sepp1, Pf4, Ctsd, Ccl8, Trem2, Cd3g, Cd8a, Tim3"	Cytotoxic CD8+T	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m2c-like"	"Itgam, Adgre1, C1qc, Sepp1, Pf4, Mrc1, Xd163"	"Tam, m2c-like"	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m2d-like"	"Itgam, Adgre1, C1qc, Sepp1, Ccl5, Cd3g, Cd8a"	Proliferating CD8+T	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	"Tam, m2-not other specified"	"Itgam, Adgre1, C1qc, Sepp1"	"Tam, m2-not other specified"	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Tumor cells	"Sox9, Csn3, Wfdc18, Lcn2, Mfge8, Phlda1, Tm4sf1, Fxyd3"	Tumor Epithelial cells	NA	NA	31251913	Cell	"Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer"	NA
Mouse	Stem cells	"Bcl6b, Id4, Pax7"	Stem cells	Tissue	NA	30026551	Nat Commun	Identification of dynamic undifferentiated cell states within the male germline	GSE107256
Mouse	Dendritic cells	"H2Aa, Flt3"	Dendritic cells	Cell line	NA	30245008	Cell	LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance	GSE118019
Mouse	Monocytes	"Mafb, Ly6c2"	Monocytes	Cell line	NA	30245008	Cell	LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance	GSE118019
Mouse	Differentiated cells	"Kit, Stra8"	Differentiated cells	Tissue	NA	30026551	Nat Commun	Identification of dynamic undifferentiated cell states within the male germline	GSE107256
Mouse	Progenitor cells	HBB-BT	Erythroid progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Glial cells	Sox10	Glial cells	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Hematopoietic cells	Ptprc	Hematopoietic cells	Tissue	NA	33298926	Nat commun	TGFbeta-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	GSE160687
Mouse	CD8 T cells	"Pdcd1, Eomes, Cd38"	Expanded CD8 T cells	Tissue	NA	31398344	Cell	Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade	"GSE72056, GSE131927"
Mouse	Natural killer (NK) cells	"Pd1, Pdcd1, Trail, Tfnsf10"	ILC1s	Tissue	NA	31398344	Cell	Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade	"GSE72056, GSE131928"
Mouse	Neural cells	Map2	Post-mitotic neurons	NA	NA	31523028	Cell Stem Cell	Mitigating Antagonism between Transcription and Proliferation Allows Near-Deterministic Cellular Reprogramming	GSE134732
Mouse	Luminal cells	"Prlr, Pgr, Cited1"	Hormone receptor (HR)+ luminal cells	NA	NA	31251913	Cell	"Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer"	NA
Mouse	Luminal cells	"CD26, Dpp4, CD133, Prom1"	Luminal1	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Luminal cells	Trop2	Luminal2	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Macrophages	"Wnt2, Wnt6, Wnt10a, RorB"	M1 macrophages	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Macrophages	"Mrc1, Arg1"	M2 macrophages	Cell line	NA	30245008	Cell	LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance	GSE118019
Mouse	Macrophages	"Rspo1, Fgf10, Sult1e1"	M2 macrophages	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Enterocytes	"Vil1, Mep1a, Clec2h, Lct, Cbr1, Ephx2"	Enterocytes	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Enterocytes	"Vil1, Mep1a, Clec2h, Lct, Cbr1, Ephx2"	Enterocytes	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Enteroendocrine cells	"Tph1, CcK, Chga, Chgb, Cpe"	Enteroendocrine cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Enteroendocrine cells	"Tph1, CcK, Chga, Chgb, Cpe"	Enteroendocrine cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Goblet cells	"Tff3, Manf, Muc2"	Goblet cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Goblet cells	"Tff3, Manf, Muc2"	Goblet cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Stromal cells	"Col6a2, Col1a1, Col3a1, Dcn"	Stromal cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Stromal cells	"Col6a2, Col1a1, Col3a1, Dcn"	Stromal cells	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Macrophages	"Mafb, H2Aa"	Mature TAM	Cell line	NA	30245008	Cell	LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance	GSE118019
Mouse	Macrophages	Adgre1	Macrophages	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Macrophages	"C1qc, Apoe"	Tumor associated macrophages	NA	NA	32632238	Nat Methods	ZipSeq:barcoding for real-time mapping of single cell transcriptomes	GSE145502
Mouse	Megakaryocytes	"VWF, GATA2"	Megakaryocyte_basophil progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Monocytes	"IRF8, LY86"	Monocyte progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Neutrophils	"MPO, CTSG"	Neutrophil progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Neutrophils	"Itgam, Hp, Ly6c2, Msrb1, Chil3"	Neutrophils	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	CD4 T cells	CD4	CD4 T cells	Tissue	NA	32169218	Cell	Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.	GSE144507
Mouse	CD8 T cells	CD8a	CD8 T cells	Tissue	NA	32169218	Cell	Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.	GSE144507
Mouse	Myeloid cells	"Adgre1, Lyz2, Itgax"	Myeloid cells	Tissue	NA	32169218	Cell	Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.	GSE144507
Mouse	Natural killer T (NKT) cells	"CD3e, Nkg7"	Natural killer T (NKT) cells	Tissue	NA	32169218	Cell	Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.	GSE144507
Mouse	Basal cells	"Trp63, Krt5, Krt14"	Basal cells	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Endothelial cells	CD31	Endothelial cells	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Endothelial cells	"CD31, Prox1"	Lymphatic endothelial cells (LECs)	NA	NA	32355025	Science	Regenerative potential of prostate luminal cells revealed by single-cell analysis	NA
Mouse	Phagocytes	"Ptprc, Cx3cr1, Fyb, Hck"	Phagocytes	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	Phagocytes	"Ptprc, Cx3cr1, Fyb, Hck"	Phagocytes	Tissue	NA	31723262	Nature	Activity of caspase-8 determines plasticity between cell death pathways	GSE132134
Mouse	B cells	Cd79a	B cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	CD4 T cells	"Cd4, Foxp3"	CD4 T cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	CD8 T cells	Cd8a	CD8 T cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Dendritic cells	"Siglech, Cd209a"	Plasmacytoid DCs	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Dendritic cells	Ccr7	Migratory DCs	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Mast cells	Cma1	Mast cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Monocytes	Ms4a4c	Monocytes	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	Stromal cells	Sparc	Stromal cells	Tissue	NA	32451497	Nat Med	Common germline variants of the Human APOE gene modulate melanoma progression and survival	NA
Mouse	T cells	"EBF1, CD19, TRBC1"	Preb and T cell progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Myeloid cells	Cxcl9	CD45 cells	NA	NA	32640238	Cell Rep	Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophagess Predicts Response to Avelumab Treatment	GSE150970
Mouse	Myeloid cells	Cd38	Myeloid cells	NA	NA	32640238	Cell Rep	Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophagess Predicts Response to Avelumab Treatment	GSE150970
Mouse	Dendritic cells	"CD74, H2-AA, H2-EB1"	Dendritic progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Lymphocyte cells	DNTT	Lymphoid progenitors	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Stem cells	"CTLA2A, HLF, CD34"	Stem cells	NA	NA	32641586	JCI Insight	Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes	NA
Mouse	Fibroblasts	"Fap, Pdpn"	Cancer associated fibroblasts (CAFS)	Tissue	NA	33298926	Nat commun	TGFbeta-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	GSE160687
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	NA	33298926	Nat commun	TGFbeta-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	GSE160687
Mouse	Mesenchymal cells	"Thy1, Fap"	Mesenchymal cells	Tissue	NA	33298926	Nat commun	TGFbeta-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	GSE160687
Mouse	Dendritic cells	"Syngr2, Cd209a, Ccr2"	Monocyte-derived dendritic cells	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Monocytes	"Itgam, Ccr2, Tgfbi, Fcgr2b"	Monocytes	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Natural killer (NK) cells	"Ncr1, Klra7, Klre1"	Natural killer (NK) cells	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Stromal cells	"Col3a1, Sparc"	Stromal cells	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Lymphocyte cells	"Cd3e, Cd3g, Thy1, Cd8a, Cd4, Ikzf2"	T lymphocytes	Tissue	NA	33301708	cell	Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity	GSE160687
Mouse	Neural cells	"CTIP2, TBR1"	Deeper layer neuron	Tissue	Neocortex	33053360	Cell Rep	LRIG1-Mediated Inhibition of EGF Receptor Signaling Regulates Neural Precursor Cell Proliferation in the Neocortex	"GSE107122, GSE152281"
Mouse	Nsc	"Prom1, Gfap"	Nsc	Tissue	Neocortex	33053360	Cell Rep	LRIG1-Mediated Inhibition of EGF Receptor Signaling Regulates Neural Precursor Cell Proliferation in the Neocortex	"GSE107122, GSE152281"
Mouse	Melanoblasts	"Mitf, Pmel, Dct"	Melanoblasts	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Neural tube cells	"Olig3, FoxB1"	Neural tube cells	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Placodal cranial sensory ganglia	Phox2b	Placodal cranial sensory ganglia	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neuronal cells	"Sox9, Foxd3, Ets1"	Premigratory neural crest	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Neuronal cells	"Sox9, Foxd3, Ets1"	Premigratory neural crest	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Progenitor cells	"Tubb3high, Elavl4"	Bipotent progenitors	Tissue	Neural crest	31442438	Gastroenterology	"Activation of Hedgehog Signaling Promotes Development of Mouse and Human Enteric Neural Crest Cells, Based on Single-Cell Transcriptome Analyses"	NA
Mouse	Glial cells	"Mpz, Fabp7, Zfp488, Plp1, Sox10"	Early glial cells	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Endothelial cells	"Emcn, Ecscr, Cdh5"	Blood vessel-derived endothelial cells	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Prdm12	Jugular neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	"Tubb3, Snap25, Uchl1"	Neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	Slc17a6	Peripheral sensory neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Neural cells	"Hand2, Tbx20, Ecel1"	Sympathetic neurons	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Glial cells	"Fabp7, Plp1, Sox10"	Glial progenitors	Tissue	Neural crest	31442438	Gastroenterology	"Activation of Hedgehog Signaling Promotes Development of Mouse and Human Enteric Neural Crest Cells, Based on Single-Cell Transcriptome Analyses"	NA
Mouse	Mesenchymal cells	"Prrx1, Twist1"	Mesenchymal cells	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Neural cells	"Foxd3, Sox9, Sox10, Ets1"	Neural crest cells	Tissue	Neural crest	31171666	Science	Spatiotemporal structure of cell fate decisions in murine neural crest.	GSE129114
Mouse	Neural cells	"Acta2, Actg2, Tagn, Hand1, Snail2, Sox10"	Neural crest cells	Tissue	Neural crest	31442438	Gastroenterology	"Activation of Hedgehog Signaling Promotes Development of Mouse and Human Enteric Neural Crest Cells, Based on Single-Cell Transcriptome Analyses"	NA
Mouse	Glial cells	"Apoe, Fabp7, Dbi"	Satellite glial cells	Tissue	Neural crest	31116992	Cell Rep	An Atlas of Vagal Sensory Neurons and Their Molecular Specialization	GSE124312
Mouse	Tissue retention	"Itgal, Itga4"	Tissue retention	Tissue	Neurogenic niche	31270459	Nature	Single-cell analysis reveals T cell infiltration in old neurogenic niches	NA
Mouse	T cells	"Cd62l, Cd44"	Memory cells	Tissue	Neurogenic niche	31270459	Nature	Single-cell analysis reveals T cell infiltration in old neurogenic niches	NA
Mouse	T cells	"Cd69, Xcl1"	Activated T cells	Tissue	Neurogenic niche	31270459	Nature	Single-cell analysis reveals T cell infiltration in old neurogenic niches	NA
Mouse	Fenestrated vascular endothelia	"Emcn, Flt1, Plvap"	Fenestrated vascular endothelia	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Fenestrated vascular endothelia	"Emcn, Flt1, Plvap"	Fenestrated vascular endothelia	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Il cells	"Pomc, Pcsk2"	Il cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Il cells	"Pcsk2, Scg2, Chga"	Il cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Il cells	"Pomc, Pcsk2"	Il cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Il cells	"Pcsk2, Scg2, Chga"	Il cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Vascular leptomeningeal cells	"Ogn, Lum, Dcn"	Vascular leptomeningeal cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Astrocytes	Apoe	Astrocytes	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Astrocytes	Apoe	Astrocytes	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Epithelial cells	"Krt18, Krt8, Clu"	Epithelial cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Epithelial cells	"Krt18, Krt8, Clu"	Epithelial cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Vegfa, Gja1"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Col25a1, Scn7a, Srebf1"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	Apoe	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Gja1, Cx43, Vegfa, Vim"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	Col25a1	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Vegfa, Gja1"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Col25a1, Scn7a, Srebf1"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	Apoe	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	"Gja1, Cx43, Vegfa, Vim"	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Pituitary cells	Col25a1	Pituitary cells	Tissue	Neurohypophysis	31915267	ENEURO	Single-Cell Molecular and Cellular Architecture of the Mouse Neurohypophysis	GSE135704
Mouse	Hepatoblasts	Sall4	Hepatoblasts	Organoids	Olfactory bulb	32661426	Nat Methods	Investigating higher-order interactions in single-cell data with scHOT	"GSE87795, GSE90047, GSE96981"
Mouse	Myelinating-oligodendrocyte-based	Mag	Myelinating-oligodendrocyte-based	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Olfactory ensheathing cell-based	Sox10	Olfactory ensheathing cell-based	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Blood cells	Slco1c1 Pdgfrb	Blood-vessel-based	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Cholangiocytes	Epcam	Cholangiocytes	Organoids	Olfactory bulb	32661426	Nat Methods	Investigating higher-order interactions in single-cell data with scHOT	"GSE87795, GSE90047, GSE96981"
Mouse	Astrocytes	Gfap	Astrocytes	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Neural cells	"Syt1, Tubb3"	Neurons	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Oligodendrocytes	Olig2	Oligodendrocyte precursors	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Hematopoietic cells	"Aif1, Siglich, CD52, CD74, Hba a1"	Hematopoietic cells	Tissue	Olfactory bulb	30517858	Cell Rep	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons	GSE121891
Mouse	Hepatocytes	Ahsg	Hepatocytes	Organoids	Olfactory bulb	32661426	Nat Methods	Investigating higher-order interactions in single-cell data with scHOT	"GSE87795, GSE90047, GSE96981"
Mouse	Basal cells	Ascl1	Globose basal cell	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Immediate neuronal precursor (inp)	"Neurog1, Neurod1"	Immediate neuronal precursor (inp)	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Neural cells	"Omp, Gnal"	Mature olfactory sensory neuron (mosn)	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Microvillous cell (mv)	"Coch, Ascl3, Cftr, Sox9, Trpm5"	Microvillous cell (mv)	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Ms4a-expressing chemosensory receptor cell (ms4)	"Ms4a4c, Ms4a6c, Ms4a7"	Ms4a-expressing chemosensory receptor cell (ms4)	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Sustentacular cells	"Cyp2g1, Cyp1a2"	Sustentacular cells	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Basal cells	"Krt5, Trp63, Krt14"	Horizontal basal cells	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Neural cells	Gap43	Immature olfactory sensory neuron (iosn)	Tissue	Olfactory epithelia	30482691	Neuron	A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period	GSE120199
Mouse	Osteoclasts	"Acp5, Ctsk, Mmp9, Nfatc1, Dcstamp, Atp6v0d2"	Mature osteoclasts	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Neutrophils	"S100a8, S100a9, Camp, Ngp"	Neutrophils	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Osteoblasts	"Tnfrsf11a, Csf1r, Cx3cr1"	Osteoclast precursors	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	B cells	"Igkc, Ighm, Iglc1, Iglc3"	B cells	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Megakaryocytes	Pf4	Megakaryocytes	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Mesenchymal cells	"Col1a1, Col1a2, Sparc"	Mesenchymal cells	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Macrophages	"Vcam1, C1qa, Cd5l, C1qc"	Vcam1 macrophages	Cell line	Osteoclast	33288951	Nature Metabolism	Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution	GSE147174.
Mouse	Non-ovulatory gcs	"FoxI2, Esr2"	Non-ovulatory gcs	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Ovulatory cumulus gcs	Ube2c	Ovulatory cumulus gcs	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Ovulatory mural gcs	"Pgr, Snap25"	Ovulatory mural gcs	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Granulosa cells	"Wnt4, Wnt6, Kitl, Foxl2"	Pre-granulosa cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Theca cells	Cyp17a1	Theca cells	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Dendritic cells	"HLA-, DR, CD11c, CD1c, CD16"	Dendritic cells	Tissue	Ovary	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"FCN1, S100A9, VCAN, FCGR1A, FCGR1B, CD1C, FCER1A, IFITM2, CLEC10A, FCGR2B."	Monocyte-related genes and DC genes	Tissue	Ovary	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"FCN1, S100A9, VCAN, FCGR1A, FCGR1B, CD1C, FCER1A, IFITM2, CLEC10A, FCGR2B."	Monocyte-related genes and DC genes	Tissue	Ovary	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"CCR7, LAMP3, CCL19, MARCKSL1, CD83, IDO1."	DC activation genes	Tissue	Ovary	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Germ cells	"Ddx4, Dazl, Utf1, Pou5f1, Hist1h2ap"	Premeiotic germ cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Stra8"	Preleptotene (Pre-L) cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Stra8, Rec8"	Leptotene cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Sycp2, Syce3"	Zygotene cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Msh4, Mlh3, Ybx2"	Pachytene	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Topaz1, Sycp2, Ybx2, Gtsf1, Sycp3, Taf71"	Diplotene	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Sycp2l, Gtsf1, Sycp3, Taf71"	Dictyate	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Germ cells	"Ddx4, Dazl, Sycp3, Taf71, Syce3"	Dying	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Interstitial cells	"Col1a1, Mgp"	Interstitial cells	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Endothelial cells	Icam2	Endothelial cells	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Immune cells	Ptprc	Immune cells	Tissue	Ovary	32294429	Cell Rep	Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation	GSE145107
Mouse	Endothelial cells	"Cldn5, Car2, Lcn2, Cx3cr1"	Endothelial cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Epithelial cells	"Upk3b, Krt19"	Epithelial cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Mesenchymal cells	"Nr2f2, Col1a1"	Mesenchymal cells	Tissue	Ovary	32759216	Proc Natl Acad Sci U S A	Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary	GSE136441
Mouse	Cancer cells	"Krt18, Sox9"	Cancer cells	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Alpha cells	"NeuroD1, Arx"	Early-stage alpha cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Entericneuron	Ascl1	Entericneuron	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Eps	"Ngn3, Hes6"	Eps	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Extrahepaticbile ductal cells	Sox17	Extrahepaticbile ductal cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Fev-expressing cells	"Pax4, Runx1, Runx1t1, Ngn3"	First group	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Fev-expressing cells	"Chgb, Vim"	Second group	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Fevhigh	"Fev, Cck, Neurod1"	Fevhigh	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Insulin cells	"Amylase, Prss1, Ptf1a"	Acinar cell	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Mesothelial cells	"Lrrn4, Gpm6a, Nkain4, Lgals7, Msln"	Mesothelial cells	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Mesothelial cells	"Upk3b, Lrrn4"	Mesothelial cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Metaplastic cells	Sox9	Metaplastic cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Mpcs	Dlk1	Mpcs	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Mtc	"Dclk1, Vav1, Pou2f3, Cxcl1, Cxcl2"	Mtc	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Myeloid cells	"Cd177, Cxcr2, Mmp8, Arg2, Itgamhi"	Myeloid-derived suppressor cells (mdsc)	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Myeloid cells	"Mmp9, Il1r2, Il1b"	MMDSCs	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Myeloid cells	"Retnlg, Osm, Wfdc17"	GMDSCs	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Myeloid cells	"Ptprc, Cd14, Itgam, Cxcr2"	Myeloid-derived suppressor cells (mdsc)	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Pancreatic cell	"Sst, Hhex, Pdx1"	Pancreatic delta cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Pancreatic cell	"DBA lectin, CD133"	Pancreatic ductal cells	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Pancreatic cell	"Sox9, Krt19"	Pancreatic ductal cells	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Pancreatic cell	"CD9, Onecut2"	Pancreatic ductal cells	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Pancreatic cell	"Prox1, Pdx1"	Pancreatic epithelial lineage cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115936
Mouse	Pancreatic cell	"Ppy, Mafbneg, Spp1"	Pancreatic peptide-producing cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Pancreatic cell	"Pdgfra, Pdgfrb"	Pancreatic stellate cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Pancreatic cell	"Sox9, Nkx6-1, Mucin-1, EpCAM, E-Cadherin"	Pancreatic tubular epithelium	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Pdc	Siglech	Pdc	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Perivascular cells	"Pecam1, Cdh5, Lgfbp7, Cxcl12"	Perivascular 1	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Perivascular cells	"Lgfbp7, Rgs5, Fdgfrb"	Perivascular 2	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Proliferating cells	"Top2a, Mki67"	Proliferating cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	T cells	"CD4, hCD2_"	T helper cell	Organoids	Pancreas	30236153	Genome Med	Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells.	NA
Mouse	Tam	"Ptprc, H2-Ab1, Itgam, Cd14"	Tam	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Tip cells	"Ptf1a, Rbpjl, Cpa1"	Tip cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Tip cells	"Cpa1, Myc"	Tip cells	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Tumor cells	"Krt8, Krt18"	PEMT tumor cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Tumor cells	"Crabp1, Crabp2"	EMT tumor cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Beta cells	"Ins1, Ins2, Slc2a2, Nkx6-1, Pdx1, Mafa"	Beta cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Beta cells	"Ins1, Ins2, Pdx1, Iapp, Nnat, Ppp1r1a"	Beta cells	Tissue	Pancreas	30540962	Stem Cell Reports	Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors	GSE120522
Mouse	Beta cells	Ins1	Beta cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115933
Mouse	Beta cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Neurog3, Sox9, Ins2, Gcg, Sst"	Beta cells	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Endocrine cells	Ins2	Beta/endocrine cell	Tissue	Pancreas	32165492	Development	Role of nutrient-driven O-GlcNAc-post-translational modification in pancreatic exocrine and endocrine islet development	GSE131134
Mouse	Endothelial cells	CD31	Endothelial cells	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	Blood cells	Tie2	Blood cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Dendritic cells	"H2-Oa, Flt3"	CDC	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	T cells	"CD4, hCD2"	Regulatory T cells (Treg)	Organoids	Pancreas	30236153	Genome Med	Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells.	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Epithelial cells	Cdh1	Epithelial cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Immune cells	Rac2	Immune cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Wt1, Krt19, Upk3b"	Mesothelial cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Acta2, Tagln, Myl9"	VSM cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Stmn2, Mgp"	Cluster 2	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Ace2, Figf"	Cluster 4	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Barx1, Id2"	Cluster 5	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Mesenchymal cells	"Vim, Col3a1, Col1a1, Nkx2-5, Tlx1"	Cluster 9	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Acinar cells	"Amy2b, Cpa1, Ptf1a"	Acinar cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Pecam1, Cdh5, Kdr"	Endothelial cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Immune cells	Ptprc	Immune cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Fibroblasts	"PDGFR, PDPN, Il1a, Il6, Lif, Cxcl1, Csf3"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	30366930	Cancer Discov	IL1-Induced JAK/STAT Signaling Is Antagonized by TGFbeta to Shape CAF Heterogeneity in Pancreatic Ductal Adenocarcinoma	GSE114417
Mouse	Fibroblasts	"PDGFR, PDPN, Acta2, Ctgf"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	30366930	Cancer Discov	IL1-Induced JAK/STAT Signaling Is Antagonized by TGFbeta to Shape CAF Heterogeneity in Pancreatic Ductal Adenocarcinoma	GSE114417
Mouse	Epithelial cells	Epcam	Epithelial cells	Tissue	Pancreas	30366930	Cancer Discov	IL1-Induced JAK/STAT Signaling Is Antagonized by TGFbeta to Shape CAF Heterogeneity in Pancreatic Ductal Adenocarcinoma	GSE114417
Mouse	Islet cells	"Gcg, Arx"	Differentialed islet alpha cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115932
Mouse	Ductal cells	"Krt19, Hnf1b"	Ductal cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Ductal cells	Cre recombinase	Ductal cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115935
Mouse	Ductal cells	"Sox9, Anxa2, Bicc1"	Ductal cells	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Ductal cells	"Krt18, Sox9"	Ductal cells	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Ductal cells	Dclk1	Ductal cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Acinar cells	"Rbpjl, Ptf1a"	Acinar cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115934
Mouse	Mesenchymal cells	Col3a1	Mesenchymal cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Trunk cells	"Sox9, Nkx6.1, Hes1"	Trunk cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115932
Mouse	Endocrine cells	Chga	Endocrine cells	Tissue	Pancreas	30254276	Nat Commun	Lineage dynamics of murine pancreatic development at single-cell resolution.	GSE101099
Mouse	Endocrine cells	"Rbp4, Pyy, Chgb"	Endocrine cells	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Endocrine cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Sst, Cpa1, Myc, Nr5a2, Ptf1a, Sox9, Neurog3, Neurod1, Gcg, Ins2"	Endocrine cells	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Endocrine cells	Ggc	Endocrine cells	Tissue	Pancreas	32165492	Development	Role of nutrient-driven O-GlcNAc-post-translational modification in pancreatic exocrine and endocrine islet development	GSE131134
Mouse	Endocrine cells	"Arx, Pax6, Neurod1"	Endocrine cells	Tissue	Pancreas	32165492	Development	Role of nutrient-driven O-GlcNAc-post-translational modification in pancreatic exocrine and endocrine islet development	GSE131134
Mouse	Endocrine cells	Ngn3	Endocrine precursors	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115933
Mouse	Endocrine cells	"Neurog3, Pax4, Sox4, Mdk, Gadd45a"	Endocrine progenitors	Tissue	Pancreas	30540962	Stem Cell Reports	Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors	GSE120522
Mouse	Endocrine cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Sst, Cpa1, Myc, Nr5a2, Ptf1a, Sox9, Neurog3, Neurod1, Gcg, Ins2"	Endocrine progenitors	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Epithelial cells	"Hgf, Twist, Zeb1, Slug, Etv1, Postn, Vim, Tnc"	Epithelial mesenchymal transition	NA	Pancreas	33007300	Gastroenterology	Mesenchymal Plasticity Regulated by Prrx1 Drives Aggressive Pancreatic Cancer Biology	GSE93313
Mouse	Acinar cells	"Ptf1a, Cpa1, Cel, Rbpjl"	Acinar cells	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Trunk cells	Notch2	Trunk cells	Tissue	Pancreas	31160421	Development	Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.	NA
Mouse	Epithelial cells	"Cdh1, Epcam, Gjb1, Cldn3, Tjb1, Ocln"	Epithelial cells	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Fibroblasts	Cdh11	Fibroblasts	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Mesenchymal cells	"Cdh2, Cd44, Axl, Vim, S100a4, Fbln2"	Mesenchymal cells	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Myofibroblasts	"Acta2, Tagln"	Myofibroblasts	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Islet cells	"Gcg, Mafb, Arx"	Islet alpha cells	Tissue	Pancreas	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Islet cells	"Gcg, Slc38a5, Ttr"	Islet alpha cells	Tissue	Pancreas	30540962	Stem Cell Reports	Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors	GSE120522
Mouse	Islet cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Neurog3, Sox9, Ins2, Gcg, Sst"	Islet alpha cells	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Acinar cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Neurog3, Sox9, Ins2, Gcg, Sst"	Acinar cells	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Acinar cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Sst, Cpa1, Myc, Nr5a2, Ptf1a, Sox9, Neurog3, Neurod1, Gcg, Ins2"	Acinar progenitors	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Endocrine cells	"NeuroD1, Pax6"	Late-stage endocrine precursor cells	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115934
Mouse	Macrophages	"Itgam, Cd68, Csf1r, Fcgr1, Adgre1, Itgam"	CD68 Macrophages	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Macrophages	"Itgam, Cx3cr1, Adgre1, Arg1, Itgam"	CX3CR1 Macrophages	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Macrophages	Fcgr1	Macrophages	Tissue	Pancreas	30737258	EMBO J	Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution	GSE115931
Mouse	Macrophages	Arg1	M2 macrophages	Tissue	Pancreas	31335328	JCI Insight	Cellular heterogeneity during Mouse pancreatic ductal adenocarcinoma progression at single-cell resolution	GSE125588
Mouse	Macrophages	"Pf4, Ccl2, Arg1"	Mac_s1	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	Acinar cells	"Pnlip, Cpa1"	Acinar cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Ly6c1, Pi16"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Serpine2, Gpx3"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Tagln, Cthrc1"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Cxcl1, Has1"	Cancer associated fibroblasts (CAFS)	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Endothelial cells	"Pecam1, Esam"	Endothelial cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Tmem100, Dpp4"	Fibroblasts	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Fibroblasts	"Smoc2, Col15a1"	Fibroblasts	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Myeloid cells	"C1gb, Csf1r"	Myeloid cells	Tissue	Pancreas	31699795	Cancer Discov	Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy	"GSE103322, GSE129455( download)"
Mouse	Macrophages	"Mrc1, Cd274"	Mac_s2	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	Macrophages	"Plac8, Fas, Ms4a4c, Ly6i, Cd9"	Mac_s3	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	Macrophages	"Emr1, C1qa"	Macrophages	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Macrophages	"CD68, CD163, MRC1, CD207, Apoe, Lyz2, Arg1"	Macrophages	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	CD4 T cells	NA	"Lag3, Pdcd1 (PD-1), Ctla4, Icos"	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD4 T cells	NA	"CD44, Cd200, Ccr7"	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Ly6c2, Mx1, Ifit2"	CD8_s2	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Sell, Fam101b, Ccr7"	CD8_s3	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Pim3, Ing2"	CD8_s4	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Gzmk, Tox"	CD8_s5	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Gzmc, Gzmd, Prf1, Gzmf"	CD8_s6	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Serpinb1a, Il18r1, Cxcr3"	CD8_s7	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	CD8 T cells	"Apoe, C1qa, C1qc, Lgmn"	CD8_s8	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	Acinar cells	Try4	Acinar cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	B cells	Cd79a	B cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Epithelial cells	Krt19	Epithelial cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Fibroblasts	Pdgfra	Fibroblasts	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Myeloid cells	"Itgam, Cd14, Fcgr3, S100a8, Ly6g"	MDSCs	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Macrophages	"Itgam, Cd68, Adgre1, Mrc1"	Macrophages	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Dendritic cells	"Itgax, H2-Eb1, Batf3, Itgae, Clec9a"	Dendritic cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Monocytes	"Itgax, Ly6c2"	Monocytes	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Natural killer (NK) cells	"Ptprc, Nkg7"	Natural killer (NK) cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	Progenitor cells	"Pdx1, Cdh1, Ctrb1, Pnliprp1, Sst, Cpa1, Myc, Nr5a2, Ptf1a, Sox9, Neurog3, Neurod1, Gcg, Ins2"	Multipotent or bipotent progenitors	Tissue	Pancreas	31412250	Cell Rep	TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation	GSE134184
Mouse	Epithelial cells	"EPCAM, KRT19, SPP1, CFTR"	Exocrine cells	Tissue	Pancreas	31932696	Nature Genetics	Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution	EGAS00001002543.
Mouse	Epithelial cells	"EPCAM, KRT19, GCG, INS"	Endocrine cells	Tissue	Pancreas	31932696	Nature Genetics	Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution	EGAS00001002543.
Mouse	Fibroblasts	"THY1, ACTA2"	Fibroblasts	Tissue	Pancreas	31932696	Nature Genetics	Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution	EGAS00001002543.
Mouse	Immune cells	"PTPRC, CD33"	Immune cells	Tissue	Pancreas	31932696	Nature Genetics	Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution	EGAS00001002543.
Mouse	B cells	"Cd19, Cd79a, Cd79b"	B cells	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Dendritic cells	"MHCII, Batf3, H2-Ab1, Cd74"	Batf3 MHCII+ DC	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Dendritic cells	"MHCII, Itgae, Ab1"	CD103 MHCII+ DC	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	Acinar cells	Amy1	Acinar cells	Tissue	Pancreas	32165492	Development	Role of nutrient-driven O-GlcNAc-post-translational modification in pancreatic exocrine and endocrine islet development	GSE131134
Mouse	B cells	"Cd79a, Cd79b"	B cells	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Endothelial cells	"Kdr, Pecam1"	Endothelial cells	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Mesenchymal cells	"Pdgfrb, Pdgfa"	Mesenchymal cells	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Epithelial cells	Krt19	Pancreatic ductal epithelial cells	Tissue	Pancreas	29550076	Mol Ther	Long-Term Correction of Diabetes in Mouse by In Vivo Reprogramming of Pancreatic Ducts	GSE109113
Mouse	CD4 T cells	Tnfrsf4	CD4 T cells	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	CD8 T cells	"Ccl5, Cd8b1, Gzmk"	CD8 T cells	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Granulocytes	"Cstb, Zeb2, Hilpda"	Granulocytes	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Monocytes	"Cox8a, Ostf1"	Non-conventional Monocytes	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Monocytes	Clu	Monocytes	Tissue	Pancreas	32324594	JCI insight	CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity	GSE150176
Mouse	Plasma cells	Igj	Plasma cells	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	T cells	"CD4, FoxP3"	Treg	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	T cells	"Cd4, Gzmb, Klrg1"	Treg_s2	Tissue	Pancreas	31771616	J Hematol Oncol	Single-cell RNA sequencing reveals compartmental remodeling of tumorinfiltrating immune cells induced by antiCD47 targeting in pancreatic cancer	NA
Mouse	T cells	"Ptprc, Cd3e, Cd4, Foxp3"	Regulatory T cells (Treg)	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	T cells	"Ptprc, Cd3e, Cd4, Foxp3"	Regulatory T cells (Treg)	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Acinar cells	Spink1	Acinar cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	B cells	"H2-Ab1, Ma4a1, Cd79a, Ptprc"	B cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	CD4 T cells	"Ptprc, Cd3e, Cd4"	CD4 T cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	CD8 T cells	"Ptprc, Cd3e, Nkg7, Cd8a"	CD8 T cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Dendritic cells	"Ptprc, Cd3e, Lyz2, Cd19, Itgax, Itgam"	SubTypes1	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Dendritic cells	"Ptprc, Cd3e, Lyz2, Cd19, Itgax, Batf3"	SubTypes2	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Endothelial cells	"Pecam1, Cdh5, Lgfbp7"	Endothelial cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Epithelial cells	"Krt8, Krt19, Lgfbp7, Col1a1"	Epithelial cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Fibroblasts	"Lgfbp7, Colla1"	Icancer-associated fibroblasts	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Fibroblasts	"Lgfbp7, Colla1, Acta2, Nc8m1"	Mycancer-associated fibroblasts	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Natural killer (NK) cells	"Ptprc, Nkg7"	Natural killer (NK) cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Tuft cells	"Dclk1, Vav1, Pou2f3"	Tuft cells	Tissue	Pancreas	32882403	Cell Mol Gastroenterol Hepatol	The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mouse	NA
Mouse	Acinar cells	Reg	Acinar cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	CD4 T cells	Il18r1	CD4 T cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Fibroblasts	Dclk1	Fibroblasts	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Immune cells	"C3, Tnf, Cxcl2, Fosl1, Il1rn, Ltb"	Immune cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Natural killer (NK) cells	Il18r1	Natural killer (NK) cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Epithelial cells	"Epcam, Krt19, Sox9"	Stomach epithelial cells	Tissue	Pancreas	32908137	Nat Commun	Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells heterogeneity	GSE141017
Mouse	Epithelial cells	"Zo1, Sox17"	Epithelial cells	NA	Pancreas	32976774	Cancer Cell	Cholesterol Pathway Inhibition Induces TGF-beta Signaling to Promote Basal Differentiation in Pancreatic Cancer	GSE156210
Mouse	Mesenchymal cells	"Vim, Zeb2, Nes"	Mesenchymal cells	NA	Pancreas	32976774	Cancer Cell	Cholesterol Pathway Inhibition Induces TGF-beta Signaling to Promote Basal Differentiation in Pancreatic Cancer	GSE156210
Mouse	CD4 T cells	"Ptprc, Cd3e, Cd4"	CD4+ T cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	CD8 T cells	"Ptprc, Nkg7, Cd3e, Cd8a"	CD8+ T cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	T cells	Cd3e	CD4- T cells CD8- T cells	Tissue	Pancreas	31911451	Cancer Discov	Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis.	GSE 140628
Mouse	T cells	"Cd3g, Cd3d, Cd3e, Cd8ah, CD103"	T cells	Tissue	Pancreas	32142650	Nat Immunol	PD-L1 engagement on T cells promotes self-tolerance and suppression of neighboring macrophages and effector T cells in cancer	GSE145905
Mouse	T cells	"Cd3e, Cd3g"	T cells	Tissue	Pancreas	32251514	J Exp Med	Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes.	GSE141786
Mouse	Sheath cells	"Tppp3, Prg4"	Sheath cells	Tissue	Patellar tendon	31768046	Nature Cell Biology	A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis	PRJNA506218.
Mouse	Telocytes	"Fmod, Tnmd, Thbs4"	Telocytes	Tissue	Patellar tendon	31768046	Nature Cell Biology	A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis	PRJNA506218.
Mouse	Progenitor cells	"Pdgfra, Ly6a"	Fibro-adipogenic progenitors	Tissue	Patellar tendon	31768046	Nature Cell Biology	A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis	PRJNA506218.
Mouse	Macrophages	"F4, F80"	Macrophages	Tissue	Patellar tendon	31768046	Nature Cell Biology	A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis	PRJNA506218.
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Patellar tendon	31768046	Nature Cell Biology	A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis	PRJNA506218.
Mouse	B cells	"CD19, CD5"	B1a B cells	Tissue	Peritoneum	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	B cells	"CD19, CD11b"	B1b B cells	Tissue	Peritoneum	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	B cells	CD19	B2 B cells	Tissue	Peritoneum	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Macrophages	"Csf1r, Adgre1, Timd4, Gata6"	Tissueresident peritoneal macrophages	Tissue	Peritoneum	31959973	Nat Microbiol	Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	GSE121521
Mouse	Monocytes	"Csf2r, Ccr2"	Monocytes	Tissue	Peritoneum	31959973	Nat Microbiol	Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	GSE121521
Mouse	Myeloid cells	Csf1r	Myeloid cells	Tissue	Peritoneum	31959973	Nat Microbiol	Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	GSE121521
Mouse	Myeloid cells	Csf2r	Myeloid cells	Tissue	Peritoneum	31959973	Nat Microbiol	Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	GSE121521
Mouse	Cort	"Pome, Tbx19, Pax7"	Cort	Tissue	Pituitary	32193873	Protein Cell	Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity	GSE146619
Mouse	Gona	"Pou1f1, Fshb, Lhb, Gnrhr"	Gona	Tissue	Pituitary	32193873	Protein Cell	Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity	GSE146619
Mouse	Gonadotropes	Lhb	Gonadotropes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Gonadotropes	"Lhb, Gnrhr"	Gonadotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Lactotropes	Prl	Lactotropes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Lactotropes	Prl	Lactotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Lbetat2 cells	"Cga, Gnrhr, Lhb"	Lbetat2 cells	Cell line	Pituitary	29487567	Front Endocrinol (Lausanne)	Regulatory Architecture of the LbetaT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone	GSE102480
Mouse	Mel	"Pomc, Tbx19, Pax7"	Mel	Tissue	Pituitary	32193873	Protein Cell	Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity	GSE146619
Mouse	Melanotropes	"POMC, Pax7"	Melanotropes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Melanotropes	Pomc	Melanotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Stem cells	Sox2	Pituitary stem cells	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Posterior lobe	Nkx2.1	Posterior lobe	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Proliferating cells	"Top2a, Mki67"	Proliferating cells	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Somatotropes	Gh	Somatotropes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Somatotropes	Gh	Somatotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Thyrotropes	Tshb	Thyrotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Corticotropes	POMC	Corticotropes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Corticotropes	"Crhr1, Tbx19"	Corticotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Corticotropes	"Crhr1, Tbx19"	Corticotropes	Tissue	Pituitary	33373440	Endocrinology	Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi	GSE153045
Mouse	Endothelial cells	Plvap	Endothelial cells	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Stem cells	Sox2	Stem cells	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Macrophages	C1qa	Macrophages	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	Pericytes	Dcn	Pericytes	Organoids	Pituitary	31444346	Nat Commun	Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening	GSE125671
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Pituitary	32515782	J Exp Med	BACH2 drives quiescence and maintenance of resting Treg cells to promote homeostasis and cancer immunosuppression	GSE128176
Mouse	Connective tissue	Col1a1	Connective tissue	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Gonadotropes	"Lhb, Fshb"	Gonadotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Lactotropes	Prl	Lactotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Melanotropes	Pomc	Melanotrope/corticotrope	NA	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Melanotropes	Pomc	Melanotrope/corticotrope	Tissue	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Melanotropes	"Pomc, Pax7"	Melanotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Stem cells	Sox2	Pituitary stem cells	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Posterior pituitary	Nkx2.1	Posterior pituitary	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Proliferating cells	Pou1f1	Proliferating pou1f1 cells	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Somatotropes	Gh	Somatotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Thyrotrope	"Cga, Gata2, Pou1f1"	Thyrotrope	Tissue	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Thyrotropes	Tshb	Thyrotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Thyrotropes	"Cga, Gata2, Pou1f1"	Thyrotropes	NA	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Cell cycling cells	"Ccne1, Cdkn1c"	Cell cycling cells	NA	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Cell cycling cells	"Ccne1, Cdkn1c"	Cell cycling cells	Tissue	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Corticotropes	"Pomc, Pax7-"	Corticotropes	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Stem cells	"Sox2, Prop1"	Stem cells	NA	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Stem cells	"Sox2, Prop1"	Stem cells	Tissue	Pituitary glands	31913463	Endocrinology	PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression	GSE142074
Mouse	Red cells	Hbb-bt	Red blood cells	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Blood cells	C1qa	White blood cells	Tissue	Pituitary glands	30335147	Endocrinology	Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types	GSE120410
Mouse	Extravillous trophoblasts cells	"HLA-G, LAIR2, DIO"	Extravillous trophoblasts cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Stomal cells	Xist	Maternal decidual stroma	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	NA	"Acta2, Wnt5b, Pdgfrb"	Fetal mesenchyme group 1	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	NA	"Gata4, Kit, Pdpn"	Fetal mesenchyme group 2	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Pro-angiogenic lineages	Vegfc	Pro-angiogenic lineages	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Syncytiotrophoblasts cells	ERVFRD-1	Syncytiotrophoblasts cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Villous cytotrophoblasts cells	"MKI67, PARP2, PAGE4, PEG10, PARP1"	Villous cytotrophoblasts cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Blood cells	"Hbb-y, Hba-x"	Blood cells	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Stromal cells	"PRL, IGFBP1"	Decidualized stromal cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Fibroblasts	TK1	Fibroblasts	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Fibroblasts	PCNA	Fibroblasts	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Natural killer (NK) cells	"NKG7, NCAM1"	Natural killer (NK) cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Fibroblasts	VIM	Pan fibroblasts3 cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Endothelial cells	"CDH5, PECAM1"	Vascular endothelial cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Epithelial cells	"KRT8, CDH1"	Endoderm epithelial cells	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Erythroblasts	TOP2A	Erythroblasts	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Macrophages	"CD163, CD14, CSF1R, CD68"	Macrophages	Tissue	Placentas	30402542	Sci Adv	A single-cell survey of the Human first-trimester placenta and decidua	NA
Mouse	Macrophages	Mrc1	Macrophages	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	B cells	"Bank1, Btla"	B cells	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Endothelial cells	"Flt4, Vegfr3"	Lymphatic endothelial cells (LECs)	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Lymphocyte cells	Igf1	Lymphocytes	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Natural killer (NK) cells	Cd244	Natural killer (NK) cells	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Endothelial cells	"Pecam1, Kdr, Tek"	Vascular endothelial cells	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	T cells	"Gzmc, Slamf1, Cd84"	T cells	Tissue	Placentas	33141023	eLife	Single nuclei RNA-seq of Mouse placental labyrinth development	GSE152248
Mouse	Tumor cells	"p16Ink4a, p19Arf, p21Cip1, p27kip1, Pai-1"	Senescent Tumor cells	NA	Prostate	33186519	Cancer Cell	Senescence Reprogramming by TIMP1 Deficiency Promotes Prostate Cancer Metastasis	E-MTAB-9578
Mouse	Luminal cells	"Ck8, Ck18"	Luminal cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Luminal cells	"Ck8, Ck18"	Luminal cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Luminal cells	"Ck8, Ck18"	Luminal cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Macrophages	"Clec4e, Arg1, Ccl4, Retnla"	Macrophages	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Neuroendocrine cells	"Syp, Chga"	Neuroendocrine cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Basal cells	"Trp63, Ck5"	Basal cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Endothelial cells	"Cdh5, Kdr, Pecam1"	Endothelial cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Lymphocyte cells	"Ly6c2, Mzb1"	Lymphocytes	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Stromal cells	"Col1a1, Col1a2, Col3a1, Mmp2"	Stromal cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Epithelial cells	"Svs3a, Svs1"	Seminal vesicle epithelial cells	Tissue	Prostate	32807988	Nat Genet	Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	NA
Mouse	Basal cells	Trp63	Prostate basal cell	Organoids	Prostate	32934023	Cancer Res	Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection	GSE157413
Mouse	Epithelial cells	Epcam	Epithelial cells	NA	Prostate	33186519	Cancer Cell	Senescence Reprogramming by TIMP1 Deficiency Promotes Prostate Cancer Metastasis	E-MTAB-9578
Mouse	Endothelial cells	"Pecam1, Cdh5"	Endothelial cells	Tissue	Pulmonary	29858212	J Cell Biol	Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis	NA
Mouse	Monocytes	"Ccl2, Ccr2, Ly6c2, Mrc1, Itgax, Cx3cr1, Csf1r"	Cells of monocyte lineage	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Early rpcs	"Fgf15, Sfrp2"	Early rpcs	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Early rpcs	"Fgf15, Sfrp2"	Early rpcs	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Gabaergic and starburst amacrine cells	Gad1	Gabaergic and starburst amacrine cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Ganglion cells	"Pou4f2, Thy1, Nefl"	Ganglion cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Glycinergic amacrine cells	Slc6a9	Glycinergic amacrine cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Endothelial cells	PNAd	High endothelial venules	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Imc9 cancer cells	"Mgp, Fkbp11, Cdkn2a, Mrpl33"	Imc9 cancer cells	Tissue	Retina	30797773	Cell Syst	Convergent identification and interrogation of tumor-intrinsic factors that modulate cancer immunity	GSE63472
Mouse	Late rpcs	"Crym, Car2, Nfia, Nfib, Nfix"	Late rpcs	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Late rpcs	"Crym, Car2, Nfia, Nfib, Nfix"	Late rpcs	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	NA	Prkca	Rod bipolar cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	NA	Slc6a9	Glycinergic amacrine cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Neurogenic cells	"Ascl1, Neurog3"	Neurogenic cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Neurogenic cells	"Ascl1, Neurog3"	Neurogenic cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Non-rods	Nrxn3	Non-rods	Tissue	Retina	31493975	Neuron	Nucleome Dynamics during Retinal Development	GSE87064
Mouse	Perivascular cells	"Myl9, Cspg4, Pdgfrb, Myh11, Des, Acta2"	Perivascular cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Photoreceptors	Crx	Photoreceptors	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Monocytes	"Esco2, Prc1, Cenpe, Ckap2I, Hmmr, Shcbp1, PIk1, Pbk, Ska1, Kif11"	Replicating monocyte	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Epithelial cell	Rpe65	Retina pigment epithelium	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Ganglion cells	Pou4f1	Retinal ganglion cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Ganglion cells	"Pou4f1, Sncg, Pou4f2, Tfap2d"	Retinal ganglion cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Ganglion cells	"Slc17a6, Rbpms, Pou4f1, Pou4f2, Pou4f3"	Retinal ganglion cells	Tissue	Retina	31784286	Neuron	Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes	GSE137400
Mouse	Ganglion cells	"Sncg, Pou4f1, Nrn1, Slc17a6"	Retinal ganglion cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Ganglion cells	"Rbpms, Pou4f1, Thy1, Slc6a9, Nefl, Nefm, Sncg, Slc17a6, Pax6"	Retinal ganglion cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Ganglion cells	"Slc17a6, Sncg"	Retinal ganglion cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Ganglion cells	"Slc17A6, Pax6"	Retinal ganglion cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Ganglion cells	"Isl1, Pou4f2, Pou6f2, Elavl4"	Retinal ganglion cells	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Epithelial cell	Rpe65	Retina pigment epithelium	Tissue	Retina	31676603	Journal of Neuroscience	Disrupted Blood-Retina Lysophosphatidylcholine Transport Impairs Photoreceptor Health But Not Visual Signal Transduction	NA
Mouse	Epithelial cell	"Ttr, Ptgds, BEST1, RLBP1, LRAT, RPE65, RDH5, TYRP1, KRT18, RDH10, BMP4, RBP1"	Retina pigment epithelium	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Bipolar cells	"Prkca, Vstm2b, Prdm8, Pcp2"	Rod bipolar cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Bipolar cells	"Trpm1, Grm6, Sebox, Prkca, Vstm2b, Otx2, Vsx2"	Rod bipolar cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Bipolar cells	"Prkca, Lrtm1"	Rod bipolar cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Rods	Rho	Rods	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Rods	Pde6a	Rods	Tissue	Retina	31493975	Neuron	Nucleome Dynamics during Retinal Development	GSE87064
Mouse	Rods	"Rho, Gnat1, Rcvrn, Nr2e3, Nrl, Rbp3"	Rods	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Rods	"Rho, Gnat1, Cnga1, Nrl, Nr2e3"	Rods	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Rods	"Rho, Pdc, Nrl, Sag, Gnat1, Gngt1, Nr2e3, Gnb1, Cnga1"	Rods	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Rods	"Nrl, Rho"	Rods	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Rods	"Rho, Nrl, Nr2e3, Gnat1, Cngb1, Essrb, Mef2c, Gabrr2, Cplx4, Cnga1, Nxnl1"	Rods	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Rpc	"Ccnd1, Cdk4, Pax6"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"Pax6, Vsx2, Lhx2"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	Mki67	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"Pax6, Vsx2"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"cnd1, Ube2c, Fgf15, Ascl1"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"Ccnd1, Cdk4, Pax6"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"Pax6, Vsx2, Lhx2"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	Mki67	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"Pax6, Vsx2"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Rpc	"cnd1, Ube2c, Fgf15, Ascl1"	Rpc	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	S-cones	Opnsw1	S-cones	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	T cells	"Cxcr5, Bcl6, Cd40lg, Il4, Il21, Cd4"	T follicular helper cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	T cells	"Bcl6, Cxcr5, Cd4"	T follicular helper cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	T cells	"Tbx21, Cxcr6, Ifng, Tnf, Stat4, Cd4"	T helper 1 cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	T cells	"T-bet, Ifng, Cxcr6, Cd4"	T helper 1 cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	T cells	"Il17a, Il17f, Rorc, Stat3, Cd4"	T helper 17 cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Bipolar cells	"Vsx2, Sebox, Cabp5, Vsx1"	Cone bipolar cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Bipolar cells	Otx2	Bipolar cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Bipolar cells	"Pkc, Vsx2, Isl1"	Bipolar cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Bipolar cells	Otx2	Bipolar cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Bipolar cells	"Pkc, Vsx2, Isl1"	Bipolar cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Bipolar cells	"Vsx2, Grm6, Grik1"	Bipolar cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Bipolar cells	"Trpm1, Vsx1, Isl1, Gsg1, Sox6"	Bipolar cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Bipolar cells	"Vsx2, Otx2, Grm6, Prkca, Trpm1, Grik1, Vsx1, Cabp5, Scgn, Sebox"	Bipolar cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Bipolar cells	Vsx2	Bipolar cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Bipolar cells	"Cabp5, Grm6, Isl1, Otx2, Vsx2, Slc1a2, Lhx3"	Bipolar cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Monocytes	"Acp5, Lyz2, Lgals3, Ms4a7, Apoe"	CCR2low monocytes	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Bipolar cells	"Scgn, Grik1, Vsx1, Lhx4, Glra1, Fezf2, Zfhx4, Otx2, Vsx2"	Cone bipolar cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Bipolar cells	"Lrtm1, Grik1"	Cone bipolar cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Cones	"Otx2, Crx, Thrb, Rbp4"	Cone photoreceptors	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Cones	Pde6h	Cone photoreceptors	Tissue	Retina	31493975	Neuron	Nucleome Dynamics during Retinal Development	GSE87064
Mouse	Cones	"Arr3, Gnat2, Opn1mw, Opn1sw"	Cone photoreceptors	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Cones	"Arr3, Rcvrn, Gnat2, Gngt2, Opn1sw, Opn1mw, Pde6h, Guca1a"	Cone photoreceptors	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Cones	"Opn1mw, Opn1sw, Arr3, Gnat2, Cabp5, Rxrg, Thrb"	Cone photoreceptors	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Cones	"Opn1sw, Opn1mw, Gnat2, Arr3, Pde6h"	Cones	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Cones	"Arr3, Pde6h"	Cones	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Cones	Opn1mw	Cones	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Amacrine cells	"Tfap2b, Elavl3, Gad1, Gad2"	GABAergic amacrine cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Astrocytes	Pdgfralpha	Astrocytes	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Endothelial cells	"Icam2, Kcnj8"	Endothelial cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Microglia cells	Mpeg1	Microglia cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Myeloid cells	"Cd14, Fcgr3, Cd16, Fcgr2b, Cd32, Itgam, Cd11b"	Myeloid cells	Tissue	Retina	30797773	Cell Syst	Convergent identification and interrogation of tumor-intrinsic factors that modulate cancer immunity	GSE63472
Mouse	T cells	"S1pr1, Cd3, Cd4"	Effector T cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Amacrine cells	Tfap2b	Amacrine cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Amacrine cells	Pax6	Amacrine cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Amacrine cells	Tfap2b	Amacrine cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Amacrine cells	Pax6	Amacrine cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Amacrine cells	"Tfap2a, Pax6, Gad1"	Amacrine cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Astrocytes	"Pax2, S100b"	Astrocytes	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Endothelial cells	"Tie1, Cldn5"	Endothelial cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Horizontal cells	Onecut2	Horizontal cells	Tissue	Retina	30645148	FASEB Journal	Conditional deletion of Des1 in the Mouse retina does not impair the visual cycle in cones.	NA
Mouse	Horizontal cells	"Lhx1, Prox1"	Horizontal cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Horizontal cells	"Lhx1, Prox1"	Horizontal cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Horizontal cells	"Calb1, Lhx1"	Horizontal cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Horizontal cells	"Lhx1, Onecut1"	Horizontal cells	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Horizontal cells	"Lhx1, Prox1, Pax6"	Horizontal cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Horizontal cells	"Lhx1, Calb1, Gja10, Onecut1"	Horizontal cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Horizontal cells	"Lhx1, Onecut1, Onecut2, Calb1, Rcvrn, Prox1, Ntrk1, Lim2, Calb2"	Horizontal cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Horizontal cells	Lhx1	Horizontal cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Horizontal cells	"Lhx1, Pax6"	Horizontal cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Horizontal cells	"Lhx1, Pax6, Calb2, Prox1"	Horizontal cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Amacrine cells	"Onecut2, Prox1"	Amacrine cells	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Monocytes	"Atp6v0d2, F7, Pla2g2d, Mmp13, Tmem26, Fabp4, Mmp12"	Macrophage-committed monocytes	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Macrophages	"H2-Aa, Cd74, H2-Ab1, H2-Eb1, H2-DMb1, Il1b, Tgfbi, Ctsc"	Inflammatory macrophages	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Astrocytes	Pdgfra	Astrocytes	Tissue	Retina	31676603	Journal of Neuroscience	Disrupted Blood-Retina Lysophosphatidylcholine Transport Impairs Photoreceptor Health But Not Visual Signal Transduction	NA
Mouse	Endothelial cells	Tie1	Vascular endothelial cells	Tissue	Retina	31676603	Journal of Neuroscience	Disrupted Blood-Retina Lysophosphatidylcholine Transport Impairs Photoreceptor Health But Not Visual Signal Transduction	NA
Mouse	Macrophages	"Fcrls, Trem2, P2ry12, Slc2a5, Hexb, Tmem119, IBA1, Aif1)"	Macrophage_microglia	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Macrophages	"Atp6v0d2, F7, Pla2g2d, Mmp13, Tmem26, Fabp4, Mmp12, Hexb, Trem2"	Monocyte-derived macrophages	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Macrophages	"Fcrls, Xylt2, Cxcl2, Hgsnat, Hpgd, Lyve1, Adrb2, Bmp2, Pf4, Gm43603"	Perivascular macrophage	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Amacrine cells	"Gad1, Gad2, Slc6a1, Slc6a9"	Amacrine cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Endothelial cells	"Pecam1, Cspg4"	Endothelial cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Microglia cells	"Aif1, Tmem119, Cx3cr1, Trem2"	Microglia cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Amacrine cells	"Gad1, Slc6a9, Stx1b, Calb2, Chat, Th, Slc17a8, Ebf3"	Amacrine cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Astrocytes	"Pax2, Gfap, Vim, Glul"	Astrocytes	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	B cells	"Cd19, Ms4a1, Cd22, Cr2, Cd2, Cd24a"	B cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	CD8 T cells	"Cd8a, Cd8b1, Cd3e"	CD8 T cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	CD8 T cells	Cd8a	CD8A T cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Dendritic cells	"A530099J19Rik, Gm13373, Asgr2, Cyp26b1, Gpr33, Xcr1, Hepacam2, Gm9530, Gcsam, Cdh17"	Dendritic cell-committed monocytes	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Dendritic cells	"Ccr7, Dpp4, Clec9a, Itgae, Zbtb46, Flt3"	Dendritic cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Microglia cells	"Tmem119, P2ry12, Crybb1, Rspo1, Serpine2, Astn1, Cx3cr1, Csf1r"	Microglia cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Dendritic cells	"Flrt3, Lad1, Gm13546, Cdkn2b, Ccr7, Serpinb1a, Scin, Adcy6, Nudt17, Gm10851"	Monocyte-derived dendritic cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Monocytes	"Anxa8, Ccr2, Ly6c2"	Monocytes	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Monocytes	"Anxa8, Ly6c2, Ccr2, Slc7a2, Tnfsf13os, Fzd7, Ms4a8a, Clec4e, Chil3, Dmkn, Cd177, Nfe2, Plcb1, Hp, Thbs1, Arhgef3"	Monocytes	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Natural killer (NK) cells	"Ncr1, Klra1, Klra6, Klrb1c, Klrb1a, Klrb1b, Klrb1f"	Natural killer (NK) cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Dendritic cells	"Pir, Klk1, Angptl7, Sh3bgr, Ccdc162, Cacna1e, Emid1, Dntt, Cd300c, Klk1b27"	Plasmacytoid dendritic cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	CD4 T cells	"Cd3e, S1pr1, Ccr7, Il6ra, Lef1, Cd44, Cd69, Cd4"	Undifferentiated CD4 T cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Endothelial cells	"Cldn5, Cdh5, Pecam1, Vwf, Erg, Tek, Kdr, Flt1"	Vascular endothelial cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Muller cells	Lif	Muller cells	Tissue	Retina	31676603	Journal of Neuroscience	Disrupted Blood-Retina Lysophosphatidylcholine Transport Impairs Photoreceptor Health But Not Visual Signal Transduction	NA
Mouse	Muller cells	"Glul, Rlbp1"	Muller cells	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Muller cells	Lhx2	Muller cells	Tissue	Retina	32457148	Proc Natl Acad Sci U S A	Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice	GSE147573
Mouse	Muller cells	"Gfap, Vim, Aqp4, S100B, Aldh1l1, Glul, Rlbp1, Slc1a3, Pax6, Acsl3, Sparc, Col9a1, Spc25, Car14, Apoe, Dkk3, Itm2B, Dbi, Gpr37, Car2, Dtx2, Pax6, Clu, Ptn, Pdgfra, Hes1"	Muller cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Muller cells	"Vim, Slc3a2, Glul, Rlbp1"	Muller glia cells	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Muller cells	"Slc1a3, Apoe, Dkk3, Gpr37, Rlbp1, Rax, Hes1, Notch1, Glul"	Muller glia cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Muller cells	"Rlbp1, Glul, Apoe, Crabp1, Clu, Slc1a3, Dkk3, Crym, Gfap, Gpr37"	Muller glia cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Muller cells	"Pax6, Vsx2, Rlbp1"	Muller glia cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Muller cells	Rlbp1	Muller glia cells	Cell line	Retina	33326790	Cell Rep	Microglia Suppress Ascl1-Induced Retinal Regeneration in Mouse	GSE161394
Mouse	Muller cells	Stat1	Muller glia cells	Cell line	Retina	33326790	Cell Rep	Microglia Suppress Ascl1-Induced Retinal Regeneration in Mouse	GSE161394
Mouse	Muller cells	Dll3	Muller glia cells	Cell line	Retina	33326790	Cell Rep	Microglia Suppress Ascl1-Induced Retinal Regeneration in Mouse	GSE161394
Mouse	Muller cells	Otx2	Muller glia cells	Cell line	Retina	33326790	Cell Rep	Microglia Suppress Ascl1-Induced Retinal Regeneration in Mouse	GSE161394
Mouse	Natural killer (NK) cells	"Cd3e, Klra1, Klra6, Cd8a, Cd8b1"	Natural killer (NK) cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Neural cells	"Otx2, Cabp5"	Bipolar neurons	Tissue	Retina	32075759	Cell Rep	STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina	NA
Mouse	Neural cells	"Otx2, Cabp5"	Bipolar neurons	Tissue	Retina	32075759	Cell Rep	STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina	NA
Mouse	Neuroblasts	"Sstr2, Penk, Btg2"	Neuroblasts	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	Amacrine cells	"Tfap2a, Tfap2b, Tfap2c, Gad1, Gad2, Slc6a9, C1ql1, C1ql2"	Amacrine cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Endothelial cells	"Mgp, Myl9, Col4a1, Cdh5"	Endothelial cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Microglia cells	"Cx3cr1, Hexb, B2m, C1qa, C1qb, C1qc, Tmem119, Ctss, P2ry12, Csf1r"	Microglia cells	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Pericytes	"Tagln, Acta2"	Pericytes	Tissue	Retina	31170999	J Neuroinflammation	Reactive microglia and IL1beta/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged Mouse retina.	NA
Mouse	Pericytes	"Pdgfrb, Kcnj8"	Pericytes	Tissue	Retina	31775049	Cell Rep	Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina	GSE116426
Mouse	Pericytes	"Cldn5, Igfbp7, Col4a1, Acta2"	Pericytes	Tissue	Retina	32166783	J Neurosci Res	Single_cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors__mplications in subretinal immune regulation	"GSM3580725, GSM3580727"
Mouse	Pericytes	Kcnj8	Pericytes	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Pericytes	"Pdgfrb, Des, Cspg4, Acta2, Anpep, Rgs5, Abcc9, Kcnj8, Cd248, Dlk1, MCAM, NT5E, CD44, Angpt1"	Pericytes	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Plasma cells	"Sdc1, Prdm1, Jchain, Il6ra, Tnfrsf17, Cd24a"	Plasma cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Amacrine cells	"TFAP2B, VIP, VG1, SAC, PENK, SST, nNOS, GHRH, CRH, CCK, CA-II"	GABAergic Amacrine cells	Tissue	Retina	32457074	J Neurosci	Mouse Retinal Cell Atlas:Molecular Identification of over Sixty Amacrine Cell Types	GSE149715
Mouse	Amacrine cells	"TFAP3B, VG3, SEG, PENK, AII"	Glycinergic Amacrine cells	Tissue	Retina	32457074	J Neurosci	Mouse Retinal Cell Atlas:Molecular Identification of over Sixty Amacrine Cell Types	GSE149715
Mouse	Glia cells	"ou4f2, Isl1"	Radial glia cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Glia cells	"Isl1, Pou4f2"	Radial glia cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Glia cells	"ou4f2, Isl1"	Radial glia cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Glia cells	"Isl1, Pou4f2"	Radial glia cells	Tissue	Retina	31128945	Neuron	Single-Cell RNA-Seq Analysis of Retinal Development Identififies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specifification	GSE118614
Mouse	Amacrine cells	"Pax6, Gad1, Pax6, Slc6a9"	Amacrine cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Astrocytes	"Rlbp1, Gfap"	Astrocytes	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Fibroblasts	"Pax6, Slc6a9, Vsx2"	Fibroblasts	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	Endothelial cells	"Pecam1, Kcnj8"	Vascular endothelial cells	Tissue	Retina	32650816	Genome Biol	DISC:a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning	GSE63473
Mouse	T cells	"Foxp3, Cd4, Il10"	Regulatory T cells (Treg)	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	T cells	"Foxp3, Il2ra, Il10, Tgfb1, Cd4"	Regulatory T cells (Treg)	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Amacrine cells	"Prox1, Pax6, Stx1a, Gad2, Slc6a9, Npy, Ebf1, Nrxn2, Calb1, Calr, Pvalb, Lrrn3, Tfap2b, Mark2, Kif2c, Lims1, Fzd3"	Amacrine cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Astrocytes	"Gfap, Vim, Aqp4, S100B, Aldh1l1, Slc1a2, Slc1a3, Fgfr3, Rlbp1, Dbi, Apoe, Glul, Pak3, Clu, Ptn, Pdgfra, Gjb6, Aldoc, Ntsr2, Acsbg1, Rfx4, Pbxip1, Gli3, Gja1, Timp1, Aspg, Lcn2, Steap4, S1pr3, Hspb1, CxCl10, Cd44, Osmr, Serpina3n"	Astrocytes	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Endothelial cells	"Vwf, Cdh5, Tek, Pecam1, Flt1, Kdr, Nos3, Mcam, MMRN1, CLDN5, BMX, ANGPT2, GJA4, TIE1, ROBO4, ECSCR"	Endothelial cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Fibroblasts	"S100A4, VIM, Col13a1, Col14a1, Col1a1, Itga8, Cxcl14, Npnt, Neat1, Tcf21, Lbh, Nr2f2, Tbx2, Meox2, Pi16, Mmp3, Cygb, Rtp4, Clec3b, Dcn, Prrx1, Aebp1, Lbh, Meg3"	Fibroblasts	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Microglia cells	"Mertk, Siglech, Bcl2a1a, Adora3, P2ry12, P2ry13, Olfml3, Crybb1, Hexb, Tmem119, Cx3cr1, Tyrobp, Trem2, Gpr34, Cd74"	Microglia cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Natural killer (NK) cells	"Cd3g, Cd3d, Cd3e, Nkg7, Ncr1, Klrd1, Klrc2, Klrk1"	Natural killer (NK) cells	Tissue	Retina	32734440	Diabetologia	Single-cell transcriptome analysis of the Akimba Mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy	NA
Mouse	Progenitor cells	"Sox2, Fos, Hes"	Retinal progenitor cells	Tissue	Retina	31399471	Development	Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons	GSE122466
Mouse	T cells	"Cd3d, Cd3e, Cd3g, Il2, Cd4, Cd8a, Cd8b1, Foxp3"	T cells	Organoids	Retina	31843893	Proc Natl Acad Sci U S A	Comprehensive analysis of a Mouse model of spontaneous uveoretinitis using single-cell RNA sequencing	"GSE132229, GSM3854512_3854519"
Mouse	Microglia cells	"P2ry12, Tmem119"	Microglia cells	Cell line	Retina	33326790	Cell Rep	Microglia Suppress Ascl1-Induced Retinal Regeneration in Mouse	GSE161394
Mouse	Epithelial cell	"Aqp5, Bhlha15"	Acinar	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Krt5, Krt14, Acta2, Cnn1"	Myoepithelial	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Aqp5, Sngc, Krt14, c-kit"	Intercalated duct	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Ngf, Egf"	Granular convoluted tubules	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Slc5a5, Cftr"	Striated ducts	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Krt5, Krt14, trp63"	Basal duct cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cell	"Ascl3, Kcnma1, Slc12a2"	"Duct cell, Ascl3+"	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cells	"Epcam, Krt14, Krt15"	Basal duct cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cells	"Epcam, Krt19"	Duct cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cells	"Epcam, Sox9, Aqp5"	End bud and proacinar cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Epithelial cells	"Epcam, Acta2"	Myoepithelial cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Glial cells	Ncam1	Glial cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Macrophages	Adgre1	Macrophages	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Erythrocytes	Alas2	Erythrocytes	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Mast cells	Kit	Mast cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Natural killer (NK) cells	"Nkg7, Gzma"	Natural killer (NK) cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Neural cells	Tubb3	Neural cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Muscle cells	Acta2	Smooth muscle cells	Tissue	Salivary gland	33305192	iScience	Generation of a Single-Cell RNAseq Atlas of Murine Salivary Gland Development	GSE150327
Mouse	Beta cells	"Cp, Nkx6.1"	SC-beta Cells	Tissue	SC-beta cells	32846125	Cell Rep	Single-Cell Transcriptome Profiling Reveals beta Cell Maturation in Stem Cell-Derived Islets after Transplantation	"GSE151117, GSE139535, GSE114297"
Mouse	Myocytes	Myh6 Ctnna3 Ryr2 Rbm20 Dmd Ttn Tbx5	Sinus node myocytes	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Endocardial cells	Npr3 Cdh13 Eng Hmcn1 Gmds	Endocardial cells	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Epicardial cells	Tbx18 Wt1 Rbfox1 Kcnd2 Grip1 Plxna4 Syne2	Epicardial cells	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Adipocytes	Ucp1 Cidea Prdm16 Ppargc1b Pparg	Adipocytes	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Adipocytes	Lep Ghr Slc1a5 Pde3b Sorbs1 Acsl1 Adipor2	Adipocytes	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Adipocytes	Ghr Slc1a5 Pde3b Sorbs1 Acsl1 Adipor2	Adipocytes	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Epithelial cells	Rbfox1 Kcnd2 Grip1 Plxna4 Syne2	Epithelial cells	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Fibroblasts	Col1a1 Fbn1 Ddr2 Lama2 Lamc1 Pcsk6 Gpc6 Rbms3 4930578G10Rik	Fibroblasts 1	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Fibroblasts	Col1a1 Fbn1 Ddr2 Lama2 Lamc1 Pcsk6 Gpc6 Rbms3 Mecom 4930578G10Rik	Fibroblasts 2	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Neural cells	Zfp804b Sh3gl2 Meg3 Ano1 Sntg1 Nlgn1	Neurons	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Endothelial cells	Ptprb Icam1 Vwf Ldb2 Pecam1 Cdh5	Vascular endothelial cells	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Macrophages	Maf F13a1 Cd163 C3ar1 P2ry6 Mrc1 Mgl2 Adgre1 Dab2	Macrophages	Tissue	Sinus node	31253831	Nat Commun	Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking	GSE130710
Mouse	Bm-mscs	"LepR, Grem1"	Bm-mscs	Tissue	Skeletal muscle	31809738	Cell Stem Cell	Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration	GSE110038
Mouse	Faps	"Pdgfra, Cd34"	Faps	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Faps	"Abca8a, Plxbpc2"	Faps	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Itga7+vcam1-cell	"Itga7, Rgs5, Myl9"	Itga7+vcam1-cell	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Muscle fifiber	"Ncam1, Musk"	Neuromuscular junction-postsynaptic muscle fifiber	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Muscle fifiber	Myh7	Slow-twitch muscle fifiber	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Myonuclei	"Titin, Col22a1, Erbb4"	MTJ	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Myonuclei	"Titin, AchR, AchE5, Ano4, Hs6st2"	NMJ	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Myonuclei	"Titin, Myh9, Flnc, Runx1"	Nnknown myonuclei subpopulation	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Myonuclei	"Titin, Myh7"	Slow myonuclei	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Myonuclei	"Titin, Myh2, Myh1, Myh4"	Fast myonuclei	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Myonuclei	"Itgbl1, Thbs4"	Myonuclei	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Pericytes	"Rgs5, Pdgfrb, Mcam, Cspg4, Kcnj8"	Pericytes	Tissue	Skeletal muscle	31809738	Cell Stem Cell	Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration	GSE110038
Mouse	Satellite cells	Pax7	Satellite cells	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Tenocytes	"Scx, Tnc, Tnmd, Col1a1"	Tenocytes	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Lymphocyte cells	"Mctp1, F13a1"	B/T cells	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	B cells	"Cd19, Ms4a1, Cd22"	B cells	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Endothelial cells	"Pecam, Cdh5, Kdr"	Endothelial cells	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Glial cells	"Plp1, Kcna1, S100b, Mbp"	Glial cells	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Macrophages	"Itgam, Csf1r, Adgre1"	Macrophages	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Mesenchymal cells	"Nestin-GFP, Gli1, Grem1, Lepr, PDGFRA, Sca1, LY6A, CD34"	Mesenchymal cells	Tissue	Skeletal muscle	31809738	Cell Stem Cell	Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration	GSE110038
Mouse	Progenitor cells	Hic1	Mesenchymal progenitors	Tissue	Skeletal muscle	31809738	Cell Stem Cell	Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration	GSE110038
Mouse	Progenitor cells	"Pdgfra, Thy1, Gli1"	Mesenchymal progenitors	Tissue	Skeletal muscle	31809738	Cell Stem Cell	Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration	GSE110038
Mouse	Muscle cells	"Myod1, Vcam1, Sdc4"	Muscle stem cells	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Muscle cells	"Hs6st3, Pax7"	Muscle stem cells	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Neutrophils	"Cd14, S100a8, S100a9"	Neutrophils	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Muscle cells	Myh11	Smooth muscle cells	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Stromal cells	Dcn	Stromal cells	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Fibroblasts	Thbs4	Tendon fibroblasts	Tissue	Skeletal Muscle	32109414	Cell	Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging	GSE137869
Mouse	Pericytes	"Rein, Mmrn1"	Pericytes	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	T cells	"Cd3d, Cd3e, Cd3g"	T cells	Tissue	Skeletal muscle	30922843	Molecular Cell	High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations	GSE110878
Mouse	Endothelial cells	"Pecam1, St6galnac3"	Endothelial cells	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Muscle cells	Trpc3	Smooth muscle cells	Tissue	Skeletal muscle	33037211	Nat Commun	Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers	GSE150065
Mouse	Bulge hfscs	"Krt24, Cd34, Grem1, Id2, Tnc, Thsd1, S100a4, Sfrp1, Dkk3, Pdzrn4, Postn, Angptl7"	Bulge hfscs	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Dermal	Col1a1	Dermal	Tissue	Skin	30595533	Dev Cell	Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis	GSE122043
Mouse	Dermal condensate	"Sox2, Bmp4, Ptch1"	Dermal condensate	Tissue	Skin	30595533	Dev Cell	Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis	GSE122043
Mouse	Dying cells	mt-Co1	Dying cells	Tissue	Skin	32259486	Cell	Defining the Design Principles of Skin Epidermis Postnatal Growth	GSE146122
Mouse	Endo lymo	Lyve1	Endo lymo	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Epi	"Krt14, Sfn, Ccnb1, Cdk1"	IFE C	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Krt14, Fth1"	IFE B	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Krt10, Krtdap"	IFE SB	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Sostdc1"	UHF B/SB	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Cidea, Mgst1, Krt79, Krt17"	SG	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Cd34, Postn"	OB	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epi	"Krt14, Sfn, Id1, Id3"	HG	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Epidermal spinous cells	Krt1	Epidermal spinous cells	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Stem cells	"CD34, Fgf19"	HF inner bulge stem cells	Tissue	Skin	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Hf-associated cells	Krt17	HF-associated cells	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Imm	"Cd74, Tyrobp, Cd3e, Thy1"	TC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Imm	"Cd74, Tyrobp, C1qa, Cd209f, Ccl6"	MC1	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Imm	"Cd74, Tyrobp, Lyz1, Ccl6"	MC2	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Imm	"Cd74, Tyrobp, Ly6c2, Emilin2"	MC3	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Imm	"Cd74, Tyrobp, Cd209a, Cd74"	DC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Imm	"Cd74, Tyrobp, Cd74, Cd207, Mfge8"	LC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Infundibulum	"Sox9, Krt17, Krt79"	Infundibulum	Tissue	Skin	32259486	Cell	Defining the Design Principles of Skin Epidermis Postnatal Growth	GSE146122
Mouse	Interfollicular epidermis	"ITGA6, Krt14, Krt10, Top2a"	Interfollicular epidermis	Tissue	Skin	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Isthmus	"Gli1, Lgr6, Lrig1, Plet1, Gata6"	Isthmus	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Langerhans cells	"CD45, F4, F80"	Langerhans cells	Tissue	Skin	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Misc	"Hbb-bt, Acta1, Alas2, Hba-a1, Hba-a2, Hba-bt"	RBC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Misc	"Hbb-bt, Acta1"	SM	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Myeloid cells	IL-4Ra	Myeloid-derived suppressor cells (mdsc)	Tissue	Skin	30721153	JCI Insight	MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in Human cancers.	GSE121478
Mouse	NA	"Mrc1, Cd163"	M2	Tissue	Skin	30930146	Cell Stem Cell	A Subset of TREM2+ Dermal Macrophages Secretes Oncostatin M to Maintain Hair Follicle Stem Cell Quiescence and Inhibit Hair Growth	GSE108709
Mouse	Nc	"Enho, Tyr, Pmel, Dct, Mlana, Npy"	MEL1	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Nc	"Enho, Tyr, Pmel, Dct, Mlana, Npy, Pax3, Atp6v1g1, Rps3, Tpt1"	MEL2	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Nc	"Enho, Tyr, Cnp, Mbp, Mpz"	SC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Proliferating cells	Ccnb1 Ccnb2 Cdk1 Top2a Cdc20 Mki67 Cdca3 Birc5 Cenpf Nusap1 Ube2c	Proliferating cells	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Sebaceous gland cells	"Scd1, Mgst1, Elovl6"	Sebaceous gland cells	Tissue	Skin	32259486	Cell	Defining the Design Principles of Skin Epidermis Postnatal Growth	GSE146122
Mouse	Sebgland	"Pparg, Prdm1, Igfbp2, Mgst1"	Sebgland	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Suprabasalepd	"Grhl1, Krt10, Krt77, Mt4, Krt1, Krtdap, Calm4"	Suprabasalepd	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Suprabasalhf	"Sprr1a, Krt79, Defb6, Cst6, Alox12e"	Suprabasalhf	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Tc1	"CD45, CD90.2, CD8beta"	Tc1	Tissue	Skin	30523076	Science	Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury	NA
Mouse	Tc17	"CD45, CD90.2, CD8beta, CCR6"	Tc17	Tissue	Skin	30523076	Science	Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury	NA
Mouse	Tumor cells	"Pmel, Mlana"	Tumor cells	Tissue	Skin	30559380	Nature	Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade	GSE110746
Mouse	Tumor cells	SerpinE2	Metastatic/slow cycling cells	Tissue	Skin	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Tumor cells	Axl	Melanoma	Tissue	Skin	31685822	Nat Commun	A novel Mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling Human disease.	GSE113502
Mouse	Vg3d T cells	"CD45, Vg3, TcRgd"	Vg3d T cells	Tissue	Skin	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	ANA	"Mgst1, Msx2"	Inner layer cluster	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Pthlh, Barx2"	Suprabasal ORS(ORS SB)	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Krt6a, Wfdc18, Barx2"	Midpart companion layer (mCP)	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Apoe, Cst6, Krt79, Barx2"	Upper companion layer (uCP)	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Lgr5, Edn2, Gnmt, Sfrp1, Il11ra1"	ORS B1	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Lgr5, Il11ra1"	ORS B2	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	ANA	"Mgst1, Msx2, Lgr5, Fgf5, Porcn, Il11ra1"	Lower proximal cup population (LPC)	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Nt5e, Mcam , CD90, Icam1"	Murine dermal fibroblasts	Tissue	Skin	29080679	J Invest Dermatol	SFRP2/DPP4 and FMO1/LSP1 Define Major Fibroblast Populations in Human Skin.	NA
Mouse	Epidermal cells	"Ly6a, Klf5, Tfap2c, Gata3, Pou3f1, Ifngr1, Il1r2, Il6ra, Il33, Ndufa4l2, Serpinb2"	Epidermal cells	Tissue	Skin	32094197	Proc Natl Acad Sci U S A	The aging skin microenvironment dictates stem cell behavior	GSE124901
Mouse	Stem cells	"CD34, ITGA6, Dkk3"	HF outer bulge stem cells	Tissue	Skin	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	T cells	Cd3e	Conventional T cells	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Endothelial cells	"Pecam1, Cdh5, Vwf"	Endothelial cells	Tissue	Skin	30464171	Nat Commun	Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing	GSE112673
Mouse	Fibroblasts	"Pdgfra, Lox, Dpt"	Fibroblasts	Tissue	Skin	30464171	Nat Commun	Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing	GSE112671
Mouse	Immune cells	"CD45, H2-Aa, CD68"	Immune cells	Tissue	Skin	30464171	Nat Commun	Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing	GSE112675
Mouse	Muscle cells	"Myh11, Rgs5, Notch3"	Muscle cells	Tissue	Skin	30464171	Nat Commun	Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing	GSE112672
Mouse	T cells	"CD3e, CD8a, CD44"	Activated T cells	Tissue	Skin	30721153	JCI Insight	MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in Human cancers.	GSE121478
Mouse	T cells	"CD3e, CD8a, CD62L"	Naive T cell	Tissue	Skin	30721153	JCI Insight	MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in Human cancers.	GSE121478
Mouse	T cells	"TCRbeta, CD8"	Cytotoxic T cells	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Dendritic cells	"Batf3, Flt3, H2-Dmb2, Zbtb46"	Dendritic cells	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Dendritic cells	"Batf3, Flt3, H2-Dmb2, Zbtb46"	Dendritic cells	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Monocytes	Csf1r	Monocytes	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Natural killer (NK) cells	"Ncr1, Klrb1c"	Natural killer (NK) cells	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Granulocytes	"CD45, Ly6G"	Granulocytes	Tissue	Skin	30561324	eLife	Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging	GSE122473
Mouse	Lymphocyte cells	Thy1.2	Innate lymphoid cells (ILCs)	Tissue	Skin	30712873	Cell	Homeostatic Control of Sebaceous Glands by Innate Lymphoid Cells Regulates Commensal Bacteria Equilibrium	GSE120787.
Mouse	B cells	Ifitm1	B cells	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Crabp1	FIB-1	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Rgs5	FIB-2	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Mest	FIB-3	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Cenpa	FIB-4	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	S100a9	FIB-5	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Pecam1	ENDO	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Cadm4	SCH	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Acp5	DEN	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Fibroblasts	Lyve1	LYME	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Hematopoietic stem cells	"SCA1, c-KIT, CD150"	Hematopoietic stem cells	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Myeloid cells	"C1qb, Cd14, Cd68, Lyz2, Mafb, Pf4"	Myeloid cells	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	T cells	"Cd3d, Cd81, Icos, Maf, Nkg7, Thy1"	T-lymphocyte cells	Tissue	Skin	30737373	Nat Commun	Single-cell analysis reveals fibroblast heterogeneity and myeloid derived adipocyte progenitors in murine skin wounds	GSE113854 & GSE113605
Mouse	Microglia cells	"Apoe, Iba-1, Cx3cr1, Tmem119, Trem2"	Microglia cells	Tissue	Skin	30930146	Cell Stem Cell	A Subset of TREM2+ Dermal Macrophages Secretes Oncostatin M to Maintain Hair Follicle Stem Cell Quiescence and Inhibit Hair Growth	GSE108709
Mouse	Dendritic cells	"CD11b, Ly-6C, CD11c, MHC II"	Monocyte-derived dendritic cells	Tissue	Skin	31213601	Nat Commun	Fcmr regulates mononuclear phagocyte control of anti-tumor immunity	GSE130287
Mouse	Hematopoietic cells	Ptprc	Hematopoietic cells	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	B cells	CD19	B cells	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Dendritic cells	CD11c	Dendritic cells	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	CD4 T cells	"TCRbeta, CD4"	Effector CD4 T cells	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Monocytes	"CD11b, LyC"	Monocytes	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Natural killer (NK) cells	CD49b	Natural killer (NK) cells	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Keratinocytes	"Krt10, Krt14"	Keratinocytes	Tissue	Skin	30595533	Dev Cell	Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis	GSE122043
Mouse	Fibroblasts	Col1a1	Fibroblasts	NA	Skin	31492709	Science Immunology	Regulatory T cells in skin are uniquely poised to suppress profibrotic immune responses	NA
Mouse	Macrophages	Csf1r	Macrophages	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Macrophages	"Itgam, Adgre1"	Macrophages	Tissue	Skin	30721153	JCI Insight	MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in Human cancers.	GSE121478
Mouse	Macrophages	"Cd68, F4, F80, Csf1r, Il1b, Ccr2"	M1	Tissue	Skin	30930146	Cell Stem Cell	A Subset of TREM2+ Dermal Macrophages Secretes Oncostatin M to Maintain Hair Follicle Stem Cell Quiescence and Inhibit Hair Growth	GSE108709
Mouse	Macrophages	Cd68	Macrophages	NA	Skin	31492709	Science Immunology	Regulatory T cells in skin are uniquely poised to suppress profibrotic immune responses	NA
Mouse	Macrophages	"Itgam, Adgre2, Arg1, TGFb1, Chil3"	Pro-tumorigenic M2 state	Tissue	Skin	30721153	JCI Insight	MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in Human cancers.	GSE121478
Mouse	Macrophages	"CD11b, Adgre1"	Tumor associated macrophages	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Phagocytes	"CD11b, MerTk, CD64"	Mononuclear phagocytes	Tissue	Skin	31213601	Nat Commun	Fcmr regulates mononuclear phagocyte control of anti-tumor immunity	GSE130287
Mouse	Dendritic cells	Cd11c	Dendritic cells	Tissue	Skin	31911617	Nat Commun	Siah2 control of T-regulatory cells limits anti-tumor immunity	GSE134814
Mouse	Fibroblasts	"Gsn, Lum, Col1a1, Sparc"	Fibroblasts 1	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Dcn, Lum"	Fibroblasts 2	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Cxcl2, Gpx3"	Fibroblasts 3	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Mfap5, Plac8"	Fibroblasts 4	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Notum, Crabp1, Rasd1, Pappa2"	TDP	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Corin, Nrg2, Cntn1"	ADP	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Acta2, Tegln, Grem2"	DS2	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Fibroblasts	"Gsn, Lum, Abi3bp, Ramp1, Mylk"	DS1	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Neutrophils	"Cxcr2, G0s2"	Neutrophils	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	Neutrophils	"CD11b, Ly-6C, Ly-6G"	Neutrophils	Tissue	Skin	31213601	Nat Commun	Fcmr regulates mononuclear phagocyte control of anti-tumor immunity	GSE130287
Mouse	Neutrophils	"CD11b, Ly6G"	Neutrophils	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	Neutrophils	Ly6g	Neutrophils	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	Basal cells	Krt14	Epidermal basal cells	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Epithelial cells	"Krt14, Krt1"	Epithelial cells	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Fibroblasts	Col1a2	Fibroblasts	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Immune cells	Ptprc	Immune cells	Tissue	Skin	32187560	Cell Rep	Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics	GSE142471
Mouse	Dendritic cells	"Cd209a, Cd209d, Itgax"	Dendritic cells	Tissue	Skin	32219160	Sci Adv	Phagocytosis of Wnt inhibitor SFRP4 by late wound macrophages drives chronic Wnt activity for fibrotic skin healing	GSE141814
Mouse	Natural killer (NK) cells	"Klrb1c, Klra4"	Natural killer (NK) cells	Tissue	Skin	32414321	BMC Bioinformatics	CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments	GSE121478
Mouse	Plasmacytoid dentritic cells	"Ccr9, Ly6d"	Plasmacytoid dentritic cells	Tissue	Skin	32414321	BMC Bioinformatics	CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments	GSE121478
Mouse	B cells	CD19	B cells	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Fibroblasts	"Pdpn, Col1a1"	Fibroblasts	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Myeloid cells	"CD11b, CD11c"	Myeloid cells	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	Antigen-presenting cells (APC)	"Itgax, Itgam, Xcr1, Cd207"	Antigen-presenting cells (APC)	Tissue	Skin	32453712	JCI insight	A transcriptomic map of murine and human alopecia areata	NA
Mouse	B cells	"Cd79a, Cd19"	B cells	Tissue	Skin	32453712	JCI insight	A transcriptomic map of murine and human alopecia areata	NA
Mouse	B cells	"Cd79a, Cd79b, Cd19"	B cells	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	Dendritic cells	"Cd209a, Cd74"	Dendritic cells	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	Myeloid cells	"Adgre1, Fcgr1, Cd68"	Monocytes/macrophages	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	Natural killer (NK) cells	"Gzma, Nkg7, Il2rb, Ncr1"	Natural killer (NK) cells	Tissue	Skin	32531238	Mol Ther	Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells	P30DK116074
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Cell line	Skin	30552023	Immunity	Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-g and IL-12	GSM3090155
Mouse	T cells	"TCRbeta, CD4, Foxp3"	Regulatory T cells (Treg)	Tissue	Skin	31350177	Nature	Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell- derived interferon-gamma	GSE132748
Mouse	T cells	"Cd4, Cd25"	Regulatory T cells (Treg)	Tissue	Skin	31911617	Nat Commun	Siah2 control of T-regulatory cells limits anti-tumor immunity	GSE134814
Mouse	Fibroblasts	"Dlk1, Sca1, Ly6a"	Lwc lower dermal fifibroblasts	Cell line	Skin	32755548	Cell Stem Cell	Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing	"GSE108677, GSE131601"
Mouse	Fibroblasts	"Crabp1, Prss35"	Lwc upper dermal fifibroblasts	Cell line	Skin	32755548	Cell Stem Cell	Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing	"GSE108677, GSE131600"
Mouse	Schwann cells	"Plp1, Mbp, Sox10"	Schwann cells	Tissue	Skin	30464171	Nat Commun	Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing	GSE112674
Mouse	T cells	"Mki67, Top2a"	Actively dividing cells	Tissue	Skin	30778252	Nat Immunol	Subsets of exhausted CD8 + T cells differentially mediate tumor control and respond to checkpoint blockade	GSE122713
Mouse	T cells	"Cx3cr1, Klrc1, Klrd1"	CD8+ T cells	Tissue	Skin	30778252	Nat Immunol	Subsets of exhausted CD8 + T cells differentially mediate tumor control and respond to checkpoint blockade	GSE122713
Mouse	T cells	"Ccr7, Lef1, Sell"	Naive cells	Tissue	Skin	30778252	Nat Immunol	Subsets of exhausted CD8 + T cells differentially mediate tumor control and respond to checkpoint blockade	GSE122713
Mouse	T cells	"Cd11b, Cd11c, Cd19, Cd24, Cxcr3"	Type 1 helper T cells	Tissue	Skin	31911617	Nat Commun	Siah2 control of T-regulatory cells limits anti-tumor immunity	GSE134814
Mouse	CD8 T cells	"Cd8a, Cd8b1, Cd2, Cd4-"	CD8 T cells	Tissue	Skin	32313720	OncoImmunology	Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq	GSE116390
Mouse	T cells	"CD8, CD4"	T cells	Tissue	Skin	32433953	Cell Rep	Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth	GSE42605
Mouse	T cells	"Cd3d, Cd28, Cd4, Cd8"	T cells	Tissue	Skin	32453712	JCI insight	A transcriptomic map of murine and human alopecia areata	NA
Mouse	Fibroblasts	"Col1a1, Col3a1, Col5a1, Dcn, FBln2, Mmp2, Serpinf1, Cald1, Bmpr2, Apoe, Itgb1, Prrx1"	Fentral dermis fibroblasts	Tissue	Skin	33176144	Cell Rep	Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.	GSE159345
Mouse	Vascular cells	"Pecam1, Aqp1, Fabp4, Rgcc"	EC	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Vascular cells	"Sparcl1, Acta2, Myl9, Tpm2"	VSM	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Vascular cells	"Fxyd6, Fgl2, Lyve1, Prox1"	LV	Tissue	Skin	32109378	Cell Stem Cell	The Molecular Anatomy of Mouse Skin during Hair Growth and Rest	GSE129218
Mouse	Distal isc	Bex1	Distal isc	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Enterochromaffin cells	"Reg4, Afp"	Enterochromaffin cells	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Intestinal stem cells	Lgr5	Intestinal stem cells	Tissue	Small intestine	31092921	Nature	Tracing the origin of adult intestinal stem cells	RNA sequencing data that support the findings of this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7660.
Mouse	Label-retaining cells (lrcs)	"Lgr5, Ascl2, NFAT5, NFATc3"	Label-retaining cells (lrcs)	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	M cells	"Gp2, Spib"	M cells	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Pan-isc	Lgr5	Pan-isc	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Proliferating cells	Mki67)	Proliferating cells	Tissue	Small intestine	31195149	Cell Mol Gastroenterol Hepatol	Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice.	GSE130113
Mouse	Proximal cells	Gkn3	Proximal isc	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Villus	Ada	Villus	Tissue	Small intestine	31195149	Cell Mol Gastroenterol Hepatol	Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice.	GSE130113
Mouse	Enterocytes	"Alpi, Reg1"	Enterocytes	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Enterocytes	Gm3336	Pre-enterocytes	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Enteroendocrine cells	"Chga, Chgb"	Enteroendocrine cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Goblet cells	"Muc2, Guca2a"	Goblet cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Paneth cells	Defa	Paneth cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Stem cells	"Lgr5, Olfm4, Ascl2"	Intestinal Stem cells (ISCs)	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Stem cells	"Mki67, Tuba1b"	Cycling stem cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Amplifying cells	"Lgr5, Gjb3, Fgfbp1"	Transit amplifying cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Tuft cells	"Dclk1, Hck"	Tuft cells	Tissue	Small intestine	28467820	Nature	Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem cell self-renewal	GSE92865
Mouse	Enterocytes	Reg1	Enterocytes	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Enteroendocrine cells	"Chga, Chgb, Cck, Sct, Gip, Glp1, Pyy, Nts, Ghrl"	Enteroendocrine cells	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Goblet cells	"Muc2, Guca2a"	Goblet cells	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Paneth cells	Defa	Paneth cells	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Stem cells	"Lgr5, Olfm4, Ascl2"	Lgr5-eGFP+ stem cells	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Tuft cells	"Dclk1, Trpm5, Nrgn, Ptgs1, Rgs13"	Tuft cells	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Paneth cells	Mptx2	Paneth cells	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Tuft cells	"Il4ra, Il13ra1, Ptprc, CD45"	Tuft-2 cells	NA	Small intestine	29144463	Nature	A single-cell survey of the small intestinal epithelium	GSE92332
Mouse	Dendritic cells	"Irf8, Xcr1, Clec9a, Cd8a, Batf3, Id2, Cd24"	CDC1	Tissue	Small intestine	33207209	Immunity	Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues	E-MTAB-9522
Mouse	Dendritic cells	"Irf4, Sirpa, Clec4a4, Klf4, Rbpj, Notch2, Mgl2"	CDC2	Tissue	Small intestine	33207209	Immunity	Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues	E-MTAB-9522
Mouse	Paneth cells	"Lyz1, Defa17, Defa22, Defa24, Aug4"	Paneth cells	Tissue	Small intestine	30392957	Cell	T helper cell cytokines modulate intestinal stem cell renewal and differentiation	GSE106511
Mouse	Stem cells	"Lgr5, Ascl2, Slc12a2, Axin2, Olfm4"	Stem cells	Tissue	Small intestine	30392957	Cell	T helper cell cytokines modulate intestinal stem cell renewal and differentiation	GSE106510
Mouse	Columnar cells	"Lgr5, Olfm4, Ascl2, Tnfrsf19, Rnf43, Znrf3"	Crypt-based columnar cells (cbcs)	Tissue	Small intestine	28686870	Cell Stem Cell	Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity	GSE99457
Mouse	Amplifying cells	"Hells, Pcna"	Cycling transit amplifying cells 1	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Amplifying cells	"Mki67, Top2a"	Cycling transit amplifying cells 2	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Enterocytes	"Fabp1, Krt19"	Early enterocytes	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Enteroendocrine cells	"Neurod1, Chga"	Enteroendocrine cells	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Goblet cells	"Atoh1, Spink4"	Goblet cells	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Stem cells	NA	Stem cells	Organoids	Small intestine	30526881	Cell Stem Cell	Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	GSE119969
Mouse	Enterocytes	Alpi	Enterocytes	Tissue	Small intestine	31092921	Nature	Tracing the origin of adult intestinal stem cells	RNA sequencing data that support the findings of this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7660.
Mouse	Enteroendocrine cells	Chga	Enteroendocrine cells	Tissue	Small intestine	31092921	Nature	Tracing the origin of adult intestinal stem cells	RNA sequencing data that support the findings of this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7660.
Mouse	Goblet cells	Muc2	Goblet cells	Tissue	Small intestine	31092921	Nature	Tracing the origin of adult intestinal stem cells	RNA sequencing data that support the findings of this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7660.
Mouse	Paneth cells	Lyz1	Paneth cells	Tissue	Small intestine	31092921	Nature	Tracing the origin of adult intestinal stem cells	RNA sequencing data that support the findings of this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7660.
Mouse	Goblet cells	Muc2	Goblet cells	Tissue	Small intestine	31195149	Cell Mol Gastroenterol Hepatol	Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice.	GSE130113
Mouse	Macrophages	CD64	Macrophages	Tissue	Small intestine	33207209	Immunity	Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues	E-MTAB-9522
Mouse	Neutrophils	Ly6G	Neutrophils	Tissue	Small intestine	33207209	Immunity	Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues	E-MTAB-9522
Mouse	Cluster0	"Tnp1, Tnp2, Prm1, Prm2"	Cluster0	Tissue	Sperm	32726616	Cell Rep	PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis	"GSE136752, GEO136752"
Mouse	Cluster12	"Sycp3, Dazl"	Cluster12	Tissue	Sperm	32726616	Cell Rep	PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis	"GSE136752, GEO136752"
Mouse	Cluster6	Acrv1	Cluster6	Tissue	Sperm	32726616	Cell Rep	PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis	"GSE136752, GEO136752"
Mouse	Gliogenic cells	Fabp7	Gliogenic cell	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Mature v2a	Vsx2	Mature v2a	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Meningeal cells	Igf2	Meningeal cells	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Neurogenic cells	"Neurog3, Hes6, Neurod4"	Neurogenic cells	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Neurogenic cells	"Neurog1, Vsx1, Hes6"	Neurogenic v2a	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Phrenic motor column	Alcam	Phrenic motor column	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	T cells	"Cd3d, Cd3e, Cd3g, Cd4"	T helper cells	Tissue	Spinal cord	32149735	J Clin Invest	Angiopoietin-2 blockade ameliorates autoimmune neuroinflammation by inhibiting leukocyte recruitment into the CNS	GSE129105
Mouse	Neural cells	"D930028M14Rik, Rnd3, Meis2, Hoxd10, Hoxd11, Igfbp5, Mpped2, BC039192, Gm2694, B230209E15Rik, Nkx6-2, Hoxc10, Zfhx3, Sparcl1, Gm16551, Pou2f2, Npnt, Ctxn2, Pdzrn4, Igf1"	V2a neurons cluster 1	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Hoxc10, Hhip, Nxph4, Prdm8, Hoxd10, Hoxd11, Npas1, Bhlhe22, Lin7a, Nefl, Meis2, Asxl3, Cplx1, Tac1, C1ql3, Tox, Vamp1, Gfra2, Myo16, Thy1"	V2a neurons cluster 2	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Ecel1, Cacng3, Nppc, Gm17750, 6430710C18Rik, C630043F03Rik, Tmem65, Crabp1, Dlk1, Kctd8, Adcyap1, Esrrg, Dach2, Npy, Nwd2, AK138361, Junb, Sp8, Gbx2, Col25a1"	V2a neurons cluster 3	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Nfix, Nfib, Tcf4, AK083547, Shisa8, Kctd12, Nxph3, Satb1, Neurod2, Neurog2, 2900055J20Rik, Ebf3, Ass1, Chd7, Ier2, Ebf1, Mira, AK142161, Col8a1, AK082503"	V2a neurons cluster 4	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Neurod2, Nfib, Tcf4, Rgs3, Mfng, Neurod1, AK138361, E130114P18Rik, AK083547, Chodl, Gbx2, Sstr1, Ass1, Snca, Enc1, Sox11, Sp8, Cadm1, Gm17750, Zeb2"	V2a neurons cluster 5	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Hoxa3, Hoxa5, Hotairm1, Hoxa4, Hoxc5, Hoxc4, Lhx1os, Mab21l2, Lhx1, Hoxb5, Tac2, Hoxb8, Shox2, Hoxa1, Hoxb6, Lrba, Nkx6-2, Camk2n1, Pou3f1, Pdyn"	V2a neurons cluster 6	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Ndufb6, Rps4l, Ppia, Myl12b, Cox5a, Ndufs3, Ubb, Vps28, Mdh1, Fkbp3, Atp5h, Psmb2, Ndufa11, Calm2, Atp5o, Psmb6, Atp5g3, Ppa1, Arl2, Grpel1"	V2a neurons cluster 7	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Hoxc5, Vsnl1, Nefh, Nkx6-2, Hoxc8, Tuba4a, Hotairm1, Npnt, Asb4, Babam1, Sncg, Lynx1, Epb41l3, Hoxc4, Sema3a, Hoxc6, Fbxo2, Mgat3, Nwd2, Nrp2"	V2a neurons cluster 8	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Fabp7, Olig1, Slc29a4, Egfl8, Actb, Dpf1, Cck, Hsf2, Khsrp, Olig2, Scrg1, Pdgfra, Insig1, Gm10778, Spock1, Prrxl1, Dbi, Kdelr2, Ebf1, Iqsec1"	V2a neurons cluster 9	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Shox2, AK136276, Bcl11b, Ccdc109b, Hoxd11, AK029540, BC030500, Igsf21, Hoxa10, Nnat, Rprml, Hoxd10, Nxph4, Npas3, Cpne4, Lrp11, Npas1, Npy, C1ql2, Lhx1os"	V2a neurons cluster 10	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Scg5, Ccdc186, Lrpap1, Tmem59l, Resp18, Cst3, Atp6v0c, Hsp90b1, Sec11a, Cd81, Tmed9, Igfbpl1, Pfkp, Tmem59, Slc25a14, Grp, 9230105E05Rik, Tmem14c, Dad1, Ncam2"	V2a neurons cluster 11	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Neural cells	"Chx10, Sox14, Shox2, Lhx3, or Lhx4"	V2a interneurons	Tissue	Spinal cord	29398364	Neuron	Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control	GSE108788
Mouse	Progenitor cells	Lin28a	Early progenitor cells	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Neural cells	"Tubb3, Elavl3, Pou4f1, Lhx2, Lhx9, Barhl1, Barhl2, Atoh1, Foxd3, Lhx1, Lhx5, lsl1, Tlx3, Prrxl1, Otp, Pax8, Lbx1, Pax2, Gbx1, BhIhe22, Pax3, Pax7, Ptf1a, Gsx1, Gsx2, Lmx1b, Ascl1, Dmrt3, Wt1, Evx1, Evx2, Pitx2, En1, Lhx3, Vsx2, Sox14, Sox21, Foxn4, Vsx1"	Neurons	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Neural cells	"Sox9, Fabp7"	Late neural progenitor	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Progenitor cells	Fabp7	Late progenitor cell	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Macrophages	"Cd14, Lyz2, Ly6c2, Cd68"	Macrophages	Tissue	Spinal cord	32149735	J Clin Invest	Angiopoietin-2 blockade ameliorates autoimmune neuroinflammation by inhibiting leukocyte recruitment into the CNS	GSE129105
Mouse	Macrophages	"Mrc1, Lyve1"	Macrophages	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Neural cells	"Sox2, Lmx1a, Msx1, Msx2, Pax3, Wnt1, Olig3, Irx3, Irx5, Pax6, Pax7, Gsx2, Ascl1, Gbx2, Gsx1, Dbx2, Dbx1, Sp8, Nkx6-2, Prdm12, Nkx6-1, Foxn4, Olig2, Nkx2-2, Nkx2-9, Foxa2, Ferd3l, Arx, Shh, Lmx1b"	Neural progenitors	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Neural cells	"Elavl3, Tubb3"	Neuronal cells	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Dendritic cells	"Kmo, Flt3, Ccr7, Ccl17"	Dendritic cells	Tissue	Spinal cord	32149735	J Clin Invest	Angiopoietin-2 blockade ameliorates autoimmune neuroinflammation by inhibiting leukocyte recruitment into the CNS	GSE129105
Mouse	Granulocytes	"Retnlg, S100a8, S100a9"	Granulocytes	Tissue	Spinal cord	32149735	J Clin Invest	Angiopoietin-2 blockade ameliorates autoimmune neuroinflammation by inhibiting leukocyte recruitment into the CNS	GSE129105
Mouse	Microglia cells	"Tmem119, P2ry12, Cx3cr1"	Microglia cells	Tissue	Spinal cord	32149735	J Clin Invest	Angiopoietin-2 blockade ameliorates autoimmune neuroinflammation by inhibiting leukocyte recruitment into the CNS	GSE129105
Mouse	Neutrophils	"S100a8, S100a9"	Neutrophils	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Astrocytes	Aqp4	Astrocytes	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Microglia cells	Ctss	Microglia cells	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Neural cells	Rbfox3	Neurons	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Oligodendrocytes	Pdgfra	Oligodendrocyte progenitors	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Oligodendrocytes	Mog	Oligodendrocytes	Tissue	Spinal cord	32241803	Genes Dev	Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons	GSE146238
Mouse	Progenitor cells	Sox2	Pan-progenitor	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Progenitor cells	"Sox2, Hes5, Olig2, Hes6, Neurog2, Neurod4"	Progenitor cells	Tissue	Spinal cord	30846445	Development	Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing Mouse spinal cord	NA
Mouse	Astrocytes	"Sparcl1, GFAP"	Astrocytes	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	B cells	"Cd74, Ly6d"	B cells	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Microglia cells	"Mki67, Birc5, Stmn1, Ube2c, Mcm3, Mcm6"	Dividing microglia cells	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Monocytes	"Ccr2, Ly6c"	Monocytes	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Microglia cells	"P2ry12, Tmem119, Cd9, Sperpine2, Spp1, Fn1, Ms4a7, Ms4a6c, P2ry12, Tmem119, Siglech"	Non-dividing microglia cells	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Oligodendrocytes	"Olig1, Olig2"	Oligodendrocytes	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	T cells	"Trbc1, Trbc2"	T cells	Tissue	Spinal cord	33029008	Nature	Neonatal microglia-organized scar-free spinal cord repair	GSE150871
Mouse	Centroblast/centrocytes	"CXCR4, CD86"	Centroblast/centrocytes	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	Dln	"Il2ra, Foxp3"	N1	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	Dz	"Mki67, Ccnb2, Ccnb1"	Dz	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	CD4 T cells	"Cd4, Foxp3, Cxcr5"	Follicular T helper cells	Tissue	Spleen	32150623	J Exp Med	Trib1 regulates T cell differentiation during chronic infection by restraining the effector program	GSE143802
Mouse	Lntermediate perivascular reticular cell	"Sca-1, CD105"	Lntermediate perivascular reticular cell	Tissue	Spleen	30988302	Nat Commun	Origin and differentiation trajectories of fifibroblastic reticular cells in the splenic white pulp	NA
Mouse	Lz	Cd83	Lz	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	NA	"Il7r, Cxcr3, Tbx21, Ifng"	T3-5	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	NA	"Il2ra, Foxp3"	T6-7	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	NA	"Tcf7, Ccr7"	N2-6	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	NA	"Cxcr5, Bcl6, Tcf7"	N7-8	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	Perivascular cells	"Ly6a, Eng, Vcam1, Pdgfra"	Perivascular reticular cell	Tissue	Spleen	30988302	Nat Commun	Origin and differentiation trajectories of fifibroblastic reticular cells in the splenic white pulp	NA
Mouse	Pre-memory and memory cells	"Ccr6, Cd38, S1pr1"	Pre-memory and memory cells	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	Recycling lz/dz	Myc	Recycling lz/dz	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	T cells	"Foxp3 , Il2ra"	T regulatory cells (Treg)	Tissue	Spleen	29434354	Nature Immunology	Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.	GSE109742
Mouse	Terminally differentiated tex_cells	"Cd8, Cxcr5, Pdcd1, Tcf7, Tox, Tbx21, Gzmb"	Terminally differentiated tex_cells	Tissue	Spleen	32150623	J Exp Med	Trib1 regulates T cell differentiation during chronic infection by restraining the effector program	GSE143802
Mouse	Tex_rogenitors	"Cd8, Cxcr5, Pdcd1, Tcf7, Tox, Tbx21, Gzmb"	Tex_rogenitors	Tissue	Spleen	32150623	J Exp Med	Trib1 regulates T cell differentiation during chronic infection by restraining the effector program	GSE143802
Mouse	Til	"Tbx21, Ifng, Cxcr6"	Tl-2	Tissue	Spleen	31801070	Cell Rep	Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells	GSE124691
Mouse	Trib1 cko cells	Klrg1	Trib1 cko cells	Tissue	Spleen	32150623	J Exp Med	Trib1 regulates T cell differentiation during chronic infection by restraining the effector program	GSE143802
Mouse	Triple negative cells	"Mcam, Pdgfrb, Cspg4, Cnn1"	Triple negative cells	Tissue	Spleen	30988302	Nat Commun	Origin and differentiation trajectories of fifibroblastic reticular cells in the splenic white pulp	NA
Mouse	Triple negative cells	"Mki67, Mcm7, Cdk6, Cks2"	Triple negative cells	Tissue	Spleen	30988302	Nat Commun	Origin and differentiation trajectories of fifibroblastic reticular cells in the splenic white pulp	NA
Mouse	T cells	"Tnfrsf4 , Tnfrsf18"	Regulatory T cells (Treg) cluster 1	Tissue	Spleen	29434354	Nature Immunology	Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.	GSE109742
Mouse	T cells	"Foxp3, Il2ra"	Regulatory T cells (Treg) cluster 2	Tissue	Spleen	29434354	Nature Immunology	Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.	GSE109742
Mouse	T cells	"Ebi3, Gzmb, Ctla4"	Regulatory T cells (Treg) cluster 3	Tissue	Spleen	29434354	Nature Immunology	Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.	GSE109742
Mouse	B cells	AID	Germinal center B cells	Tissue	Spleen	30127060	J Exp Med	"Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation"	GSE117895
Mouse	B cells	Xbp1	Plasmablast	Tissue	Spleen	30127060	J Exp Med	"Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation"	GSE117895
Mouse	Natural killer (NK) cells	"Cd69, ncr1, Il2rg, Klre1, Cd28, Ilrk1, Prr7, Ccrl2, Spry2, Klrb1c"	Natural killer (NK) cells	Tissue	Spleen	30413361	Immunity	High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mouse	GSE119562
Mouse	CD4 T cells	"CD4, CD44"	CD4 T cell memory precursor	Tissue	Spleen	30638736	Immunity	The Emergence and Functional Fitness of Memory CD4 T Cells Require the Transcription Factor Thpok.	GSE121002
Mouse	CD4 T cells	"CD4, CD44"	CD4 T cell memory precursor	Tissue	Spleen	30638736	Immunity	The Emergence and Functional Fitness of Memory CD4 T Cells Require the Transcription Factor Thpok.	GSE121002
Mouse	CD4 T cells	"CD4, CD44"	CD4 T cell memory precursor	Tissue	Spleen	30638736	Immunity	The Emergence and Functional Fitness of Memory CD4 T Cells Require the Transcription Factor Thpok.	GSE121002
Mouse	CD4 T cells	"CD4, CD44"	CD4 T cell memory precursor	Tissue	Spleen	30638736	Immunity	The Emergence and Functional Fitness of Memory CD4 T Cells Require the Transcription Factor Thpok.	GSE121002
Mouse	B cells	Ms4a1	B cells	Organoids	Spleen	30862842	Nat Commun	Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis	GSE125316
Mouse	Myeloid cells	Fcer1g	Myeloid cells	Organoids	Spleen	30862842	Nat Commun	Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis	GSE125316
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Organoids	Spleen	30862842	Nat Commun	Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis	GSE125316
Mouse	B cells	Cd19	B cells	Tissue	Spleen	31205032	J Clin Invest	Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases	NA
Mouse	CD8 T cells	"Pdcd1, Ctla4, Lag3, Entpd1, TIM3"	Exhausted T cells	Tissue	Spleen	31205032	J Clin Invest	Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases	NA
Mouse	CD8 T cells	"Il7r, Ccr7, Sell, CD44"	T memory cells	Tissue	Spleen	31205032	J Clin Invest	Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases	NA
Mouse	Dendritic cells	Itgax	Dendritic cells	Tissue	Spleen	31205032	J Clin Invest	Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases	NA
Mouse	CD8 T cells	"Tcf7, Id3, Slamf6"	Progenitorlike CD8+ T cells	Tissue	Spleen	31209400	Nat Immunol	Single-cell RNA-seq reveals TOX as a key regulator of CD8 + T cell persistence in chronic infection	GSE119943
Mouse	CD8 T cells	"Bcl2, Ccr7, Id3, Sell, Tcf7"	Memory precursor cells	Tissue	Spleen	31209400	Nat Immunol	Single-cell RNA-seq reveals TOX as a key regulator of CD8 + T cell persistence in chronic infection	GSE119943
Mouse	Dendritic cells	"Mac-1, MHC-II, CD11c"	Dendritic cells	Tissue	Spleen	31358996	Nat Immunol	The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage.	NA
Mouse	Monocytes	Il1b	Monocytes	Tissue	Spleen	31471106	Immunity	Oncolytic Viruses Engineered to Enforce Leptin Expression Reprogram Tumor-Infiltrating T Cell Metabolism and Promote Tumor Clearance	GSE133699
Mouse	Natural killer (NK) cells	Klrb1c	Natural killer (NK) cells	Tissue	Spleen	31471106	Immunity	Oncolytic Viruses Engineered to Enforce Leptin Expression Reprogram Tumor-Infiltrating T Cell Metabolism and Promote Tumor Clearance	GSE133699
Mouse	Macrophages	Nos2	M1 macrophages	Tissue	Spleen	32641748	Commun Biol	Absence of central tolerance in Aire-deficient Mouse synergizes with immune-checkpoint inhibition to enhance antitumor responses	"GSE151829, GSE151830, GSE151831"
Mouse	Macrophages	Adgre1	Macrophages	Tissue	Spleen	31205032	J Clin Invest	Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases	NA
Mouse	Macrophages	"C1qa, Mmp12, Il1b"	Macrophages	Tissue	Spleen	31471106	Immunity	Oncolytic Viruses Engineered to Enforce Leptin Expression Reprogram Tumor-Infiltrating T Cell Metabolism and Promote Tumor Clearance	GSE133699
Mouse	Macrophages	Cd68	Macrophages	Tissue	Spleen	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Antigen-presenting cells (APC)	"Cd68, Cd14, Ccl6, C1qb, C1qa"	Antigen-presenting cells (APC)	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	B cells	"Cd19, Cd79b, Cd22, Cd79a"	B cells	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	B cells	Try5	Memory B cells	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	Natural killer (NK) cells	"Gzmb, Ccl5, Gzma, Ncr1"	Natural killer (NK) cells	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	B cells	"Cd79a, Cd22, Cd19"	B cells	Tissue	Spleen	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Natural killer (NK) cells	"Klrb1c, Nkg7"	Natural killer (NK) cells	Tissue	Spleen	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	Macrophages	"H2.Aa, H2.Ab1, Ly6d, Cd79a"	Macrophages	Tissue	Spleen	32929273	Nat Immunol	Meningeal gammadelta T cells regulate anxiety-like behavior via IL-17a signaling in neurons	GSE147262
Mouse	B cells	"Cd19, Cd22, Cd79a"	B cells	Tissue	Spleen	32086381	Science Immunology	Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics	GSE139125
Mouse	Monocytes	"Csf1r, Ccr2"	Monocytes	Tissue	Spleen	32086381	Science Immunology	Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics	GSE139125
Mouse	B cells	Iglc3	B cells	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	CD4 T cells	"Cd3e, Cd4, Il7r"	CD4 T cells	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	CD8 T cells	"Cd3e, Cd8, Il7r"	CD8 T cells	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	Dendritic cells	"Tlr7, Cst3, S100a4"	Dendritic cells	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	Monocytes	"Cst3, S100a4"	Monocytes	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	Natural killer (NK) cells	Nkg7	Natural killer (NK) cells	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	Neutrophils	"Ly6g, Cxcr2"	Neutrophils	Tissue	Spleen	32086381	Science Immunology	Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics	GSE139125
Mouse	Neutrophils	Itgax	Neutrophils	Tissue	Spleen	32094169	Proc Natl Acad Sci U S A	Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus	GSE142637
Mouse	B cells	Igj	Plasma cell	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	Classified using ImmGen	Germinal center cell	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	"Fcer2a, Klf2"	Follicular cell	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	"Tcf4, Crebl2"	Marginal zone cell	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	"Gfi1, Myb, Uhrf1"	Transitional cell	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	Classified using ImmGen	Plasmablast	Tissue	Spleen	32123397	Nature methods	TooManyCells identifies and visualizes relationships of single-cell clades	"GSE81861, GSE117498"
Mouse	B cells	Mzb1	B cells	Tissue	Spleen	32125286	JCI Insight	MicroRNA-146a regulates immunerelated adverse events caused by immune _heckpoint inhibitors	GSE147327
Mouse	Myeloid cells	"Csf3r, Cxcr2, Ly6g, C1qa, C1qb"	Myeloid cells	Tissue	Spleen	32125286	JCI Insight	MicroRNA-146a regulates immunerelated adverse events caused by immune _heckpoint inhibitors	GSE147327
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Spleen	32125286	JCI Insight	MicroRNA-146a regulates immunerelated adverse events caused by immune _heckpoint inhibitors	GSE147327
Mouse	Neutrophuls	"Cxcr2, II1b"	Neutrophils	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	B cells	"B220, GL7, FAS, IgD"	GC B cells	Tissue	Spleen	32396861	Cancer Cell	Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response	GSE138037
Mouse	B cells	"Cd19, Cd38, Pax5, Ptprc"	B cells	Tissue	Spleen	32444631	Nat Commun	Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4 + T Cells in COVID-19	GSE140133
Mouse	T cells	"Cd4, Foxp3, Cxcr5"	Regulatory T cells (Treg)	Tissue	Spleen	32150623	J Exp Med	Trib1 regulates T cell differentiation during chronic infection by restraining the effector program	GSE143802
Mouse	Neural cells	"Gad1, Gad2, Slc17a7, Slc17a6"	Gabaergic neurons	Tissue	Spleen	32929273	Nat Immunol	Meningeal gammadelta T cells regulate anxiety-like behavior via IL-17a signaling in neurons	GSE147262
Mouse	T cells	Cd3g	T cells	Organoids	Spleen	30862842	Nat Commun	Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis	GSE125316
Mouse	T cells	"CD8b1, Foxp3"	T cells	Tissue	Spleen	31471106	Immunity	Oncolytic Viruses Engineered to Enforce Leptin Expression Reprogram Tumor-Infiltrating T Cell Metabolism and Promote Tumor Clearance	GSE133699
Mouse	T cells	"Timeless, Cd4, Cd27, Cd3e, Cd8a"	T cells	Tissue	Spleen	31751331	PLoS biolog	Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity	GSE132642
Mouse	T cells	Cd3e	T cells	Tissue	Spleen	31754020	Genome Research	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging	GSE132901
Mouse	T cells	"Cd3, Cd4, Cd8"	T cells	Tissue	Spleen	32086381	Science Immunology	Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics	GSE139125
Mouse	T cells	"Cd3, Cd4, Cd8"	T cells	Tissue	Spleen	32125286	JCI Insight	MicroRNA-146a regulates immunerelated adverse events caused by immune _heckpoint inhibitors	GSE147327
Mouse	T cells	"Cd4, Cd8alpha, Foxp3, Cxcl9"	T cells	Tissue	Spleen	32641748	Commun Biol	Absence of central tolerance in Aire-deficient Mouse synergizes with immune-checkpoint inhibition to enhance antitumor responses	"GSE151829, GSE151830, GSE151831"
Mouse	CD8 T cells	"Cd69, Cd103, Egr1"	CD8 T cells	Tissue	Spleen	32641748	Commun Biol	Absence of central tolerance in Aire-deficient Mouse synergizes with immune-checkpoint inhibition to enhance antitumor responses	"GSE151829, GSE151830, GSE151831"
Mouse	Macrophages	Adgre1	Macrophages	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Neutrophils	S100a8	Neutrophils	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Plasmablasts	Sdc1	Plasmablasts	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	B cells	CD79a	B cells	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Dendritic cells	Flt3	Dendritic cells	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Monocytes	"Ccr2, Ly6c2"	Monocytes	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Natural killer (NK) cells	Ncr1	Natural killer (NK) cells	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	T cells	CD3e	T cells	Tissue	Splenocytes	32699843	Cell Rep Med	An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses	"GSE141111, GSE141117"
Mouse	Intermediate	"Cd44, Met, Nrp2, Kcnj13"	Intermediate	Tissue	Stria vascularis	31920542	Frontiers in Molecular Neuroscience	Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis	GSE136196
Mouse	Marginal	"Kcne1, Kcnq1, Abcg1, Heyl"	Marginal	Tissue	Stria vascularis	31920542	Frontiers in Molecular Neuroscience	Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis	GSE136196
Mouse	Spindle	"Slc26a4, P2rx2, Kcnj16"	Spindle	Tissue	Stria vascularis	31920542	Frontiers in Molecular Neuroscience	Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis	GSE136196
Mouse	Basal cells	"CLDN11, ZO-1, Sox8, Nr2f2"	Basal cells	Tissue	Stria vascularis	31920542	Frontiers in Molecular Neuroscience	Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis	GSE136196
Mouse	Ciliated ependymal	Hydin	Ciliated ependymal	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Dspn	"Drd1, Lingo2"	Dspn	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Fxop2_olfm3 neuron	"Fxop2, Olfm3"	Fxop2_olfm3 neuron	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Ispn	Drd2	Ispn	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Neuroblasts	Dcx	Migrating neuroblast	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Mural cells	Pdgfrb	Mural cells	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Opcs	NG2	Opcs	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Pv_th interneuron	"Hs3st2, Cntnap4"	Pv_th interneuron	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Secretory cells	Ttr	Secretory ependymal	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Sst_npy interneuron	Nos1	Sst_npy interneuron	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Cycling cells	Top2a	Cycling cells	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Astrocytes	Gfap	Astrocytes	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Endothelial cells	Slc2a1	Endothelial cells	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Microglia cells	Csf1r	Microglia cells	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Neural cells	NA	Neurons	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Oligodendrocytes	Mog	Oligodendrocytes	Tissue	Striatal	32681824	Neuron	Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation	GSE152058
Mouse	Acinar cells	"Bhlha15, Aqp5"	Acinar cells	Tissue	Submandibular glands	30232460	Sci Rep	Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance.	GSE113466
Mouse	Basal cells	"Trp63, Krt5, Krt14"	Basal cells	Tissue	Submandibular glands	30232460	Sci Rep	Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance.	GSE113466
Mouse	Ductal cells	"Krt7, Krt8"	Ductal cells	Tissue	Submandibular glands	30232460	Sci Rep	Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance.	GSE113466
Mouse	Ductal cells	"Krt7, Krt8, Krt18"	C5 subtype	Tissue	Submandibular glands	30232460	Sci Rep	Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance.	GSE113466
Mouse	Cell cycling cells	"Cdk1, Cenpa, Top2a"	Cell cycling cells	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Chondrocytes	"Sox6, Cd14, Chad, Chadl, Cilp, Clu, Sox9, Matn3"	Chondrocytes	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Erythrocytes	"H2-Aa, H2-Ab1"	Erythrocytes	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Fibroblasts	"Pdpn, Fap, Thy1, Sfrp2, Col11a1, Mfap4"	Fibroblasts 1	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Fibroblasts	"Pdpn, Fap, Thy1, Tnfaip6, Inhba, Prg4"	Fibroblasts 2	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Fibroblasts	"Pdpn, Fap, Thy1, Apod, Clec3b, Cd34"	Fibroblasts 3	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Fibroblasts	"Pdpn, Fap, Thy1, Top2a, Hmgb2, Cdk1"	Fibroblasts 4	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Fibroblasts	"Pdpn, Fap, Thy1, Clic5, Col22a1, Tspan15"	Fibroblasts 5	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Muscle cells	"Actn3, Tnnt3, Aldoa"	Muscle cells	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Osteoblasts	"Alpl, Bglap, Bglap2, Omd, Runx2, Sp7, Ostn"	Osteoblasts	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Pericytes	"Acta2, Notch3, Rgs5"	Pericytes	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Vascular cells	"Cdh5, Emcn, Pecam1"	Vascular cells	Tissue	Synovium	31142839	Nature	Distinct fibroblast subsets drive inflammation and damage in arthritis	GSE129087
Mouse	Tenocytes	"Scx, Fmod, Col11a1, Col1a1, Tnmd"	Tenocytes	Tissue	Tendon	31961320	eLife	Tgfbeta signaling is critical for maintenance of the tendon cell fate	GSE139558
Mouse	Endothelial cells	"HIF1a, VEGFA"	Endothelial progenitors	Cell line	Tendon	33293508	Bone Res	Mesenchymal VEGFA induces aberrant differentiation in heterotopic ossification	GSE126060
Mouse	Endothelial cells	"CD31, Tie2, CD34, CD133"	Endothelial progenitors	Cell line	Tendon	33293508	Bone Res	Mesenchymal VEGFA induces aberrant differentiation in heterotopic ossification	GSE126060
Mouse	Condensing spermatids	"Tnp2, Tnp1, Hspa1l, Prm1"	Condensing spermatids	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Spermatocytes	"Meioc, Prdm3, Top2a, Smc3"	Early spermatocytes	Tissue	Testicle	30893341	PLoS Genet	Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.	GSE121904
Mouse	Elongating spermatids	Dyrk4	Elongating spermatids	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Elongating spermatids	Tnp1	Elongating spermatids	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Elongating spermatids	"Prm3, Izumo3, Tssk6"	Elongating spermatids	Tissue	Testicle	30893341	PLoS Genet	Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.	GSE121904
Mouse	Germline pluripotency cells	"Dppa3, Nanog, Sox2"	Germline pluripotency cells	Tissue	Testicle	31243281	Nat Commun	Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage	GSE124904
Mouse	Myoid cells	Myh11	Myoid cells	Tissue	Testicle	31582414	Development	CDK2 kinase activity is a regulator of male germ cell fate.	GSE130554
Mouse	Peritubular	Vcam1	Peritubular	Tissue	Testicle	31582414	Development	CDK2 kinase activity is a regulator of male germ cell fate.	GSE130554
Mouse	Myoid cells	"PTM, Acta2"	Peritubular myoid cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Postnatal ssc	"Etv5, Id4, Lhx1, Nanos2, Ret"	Postnatal ssc	Tissue	Testicle	31243281	Nat Commun	Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage	GSE124904
Mouse	Spermatids	Tex21	Round spermatids	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Spermatids	"Acrv1, Izumo1, Catsper3, Catsper4"	Round spermatids	Tissue	Testicle	30893341	PLoS Genet	Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.	GSE121904
Mouse	Spermatocytes	Piwil1	Spermatocytes	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Spermatocytes	"Sycp1, Sycp2, Sycp3, H2afx"	Spermatocytes	Tissue	Testicle	30893341	PLoS Genet	Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.	GSE121904
Mouse	Spermatocytes	"Tdrd1, Piwil2, Meioc, Hormad1, Gpat2"	Spermatocytes 1	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Spermatocytes	"Prss43, Prss42"	Spermatocytes 2	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Spermatocytes	"Esx1, Dazl, Crabp1"	Spermatogonia	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Spermatocytes	Dmrt1	Spermatogonia	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Spermatocytes	NA	Spermatogonia	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Spermatocytes	"Zbtb16, Sall4, Sohlh1, Dmrt1"	Spermatogonia	Tissue	Testicle	30893341	PLoS Genet	Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.	GSE121904
Mouse	Spermatocytes	"Id4, Gfra1, Lhx1, Egr2, Etv5, Nanos2, Ret, Eomes"	Spermatogonial stem cell	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Terminal differentiation cells	"Kit, Stra8"	Terminal differentiation cells	Tissue	Testicle	31243281	Nat Commun	Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage	GSE124904
Mouse	Unfractionated testicular cells	Dazl	Germ cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130593
Mouse	Unfractionated testicular cells	Amh	Sertoli Cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130594
Mouse	Unfractionated testicular cells	Pecam1	Endothelial cellss	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130598
Mouse	Unfractionated testicular cells	Cd68	Macrophage	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130599
Mouse	Unfractionated testicular cells	Cnmd	Innate lymphocyte	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130600
Mouse	Unfractionatedtesticular cells	Cyp11a1	Leydig Cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130595
Mouse	Unfractionatedtesticular cells	Acta2	Pertubular myoids	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130596
Mouse	Unfractionatedtesticular cells	Igf1	Stromal cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130597
Mouse	Unfractionatedtesticular cells	Dazl	Germ cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130593
Mouse	Unfractionatedtesticular cells	Amh	Sertoli Cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130594
Mouse	Unfractionatedtesticular cells	Cyp11a1	Leydig Cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130595
Mouse	Unfractionatedtesticular cells	Acta2	Pertubular myoids	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130596
Mouse	Unfractionatedtesticular cells	Igf1	Stromal cells	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130597
Mouse	Unfractionatedtesticular cells	Pecam1	Endothelial cellss	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130598
Mouse	Unfractionatedtesticular cells	Cd68	Macrophage	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130599
Mouse	Unfractionatedtesticular cells	Cnmd	Innate lymphocyte	Tissue	Testicle	31964773	Development	Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period	GSE130600
Mouse	Progenitor cells	"Dnmt3a, Dnmt3b, Sohlh1, Sox3"	Differentiating cell progenitors	Tissue	Testicle	31243281	Nat Commun	Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage	GSE124904
Mouse	Endothelial cells	Tm4sf1	Vascular endothelial cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Germ cells	"Dazl, Id4, Rhox10, Sohlh1"	Germ cells	Organoids	Testicle	31023878	Development	Differential RA responsiveness directs formation of functionally distinct spermatogonial populations at the initiation of spermatogenesis in the Mouse	NA
Mouse	Germ cells	MVH	Germ cells	Tissue	Testicle	31582414	Development	CDK2 kinase activity is a regulator of male germ cell fate.	GSE130554
Mouse	Germ cells	"Uba1, Pgk1, Zbtb16"	Leydig cells	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Germ cells	Fabp3	Leydig cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Germ cells	NA	Leydig cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Germ cells	NA	Leydig cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Germ cells	Cyp11a1	Leydig cells	Tissue	Testicle	31582414	Development	CDK2 kinase activity is a regulator of male germ cell fate.	GSE130554
Mouse	Macrophages	Cd14	Testicular macrophages	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	B cells	"CD79A, CD79B, STK31, DAZL, ID4, NOC4L, PTRHD1"	Spermatogonia	Tissue	Testicle	32194870	Theranostics	Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis	GSE131629
Mouse	B cells	"CD79A, CD79B, SYCP1, SYCP3, REC8, SPO11"	Spermatocytes	Tissue	Testicle	32194870	Theranostics	Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis	GSE131629
Mouse	B cells	"CD79A, CD79B, PRM1, PRM23, TNP1, TNP2"	Haploid spermatids	Tissue	Testicle	32194870	Theranostics	Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis	GSE131629
Mouse	B cells	"CD79A, CD79B, HSD3B1, STAR, INSL3"	Leydig cells	Tissue	Testicle	32194870	Theranostics	Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis	GSE131629
Mouse	B cells	"CD79A, CD79B, SOX9"	Sertoli cells	Tissue	Testicle	32194870	Theranostics	Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis	GSE131629
Mouse	Progenitor cells	"Neurog3, Sox3"	Progenitor cells	Tissue	Testicle	31243281	Nat Commun	Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage	GSE124904
Mouse	Sertoli cells	Tex19.2	Sertoli cells	Tissue	Testicle	29695820	Sci Rep	Characterization of germ cell differentiation in the male Mouse through single-cell RNA sequencing	NA
Mouse	Sertoli cells	Cldn11	Sertoli cells	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Sertoli cells	Wt1	Sertoli cells	Tissue	Testicle	31582414	Development	CDK2 kinase activity is a regulator of male germ cell fate.	GSE130554
Mouse	Progenitor cells	"Neurog3, Rarg, Nanos3, Lin28a, Upp1"	Spermatogonial progenitor	Tissue	Testicle	30890697	Nat Commun	Staged developmental mapping and X chromosome transcriptional dynamics during Mouse spermatogenesis	NA
Mouse	Natural killer T (NKT) cells	"Itm2a, Sox4, Egr2"	Invariant nkt (inkt) precursors	Tissue	Thymic	33288744	Nat Commun	Thymic iNKT single cell analyses unmask the common developmental program of Mouse innate T cells	"GSE152786, GSE160518"
Mouse	Natural killer T (NKT) cells	"Rorc, Ccr6, Zbtb16"	INKT17 cells	Tissue	Thymic	33288744	Nat Commun	Thymic iNKT single cell analyses unmask the common developmental program of Mouse innate T cells	"GSE152786, GSE160518"
Mouse	Natural killer T (NKT) cells	"Il2rb, Tbx21, Ifng"	INKT1 cells	Tissue	Thymic	33288744	Nat Commun	Thymic iNKT single cell analyses unmask the common developmental program of Mouse innate T cells	"GSE152786, GSE160518"
Mouse	Natural killer T (NKT) cells	"Zbtb16, Gata3, Cd4, Il4"	INKT2 cells	Tissue	Thymic	33288744	Nat Commun	Thymic iNKT single cell analyses unmask the common developmental program of Mouse innate T cells	"GSE152786, GSE160518"
Mouse	Natural killer T (NKT) cells	"Cd24a, Ki67, Zbtb16, Rorc, Tbx21"	Mature Natural killer T (NKT) cells	Tissue	Thymic	33288744	Nat Commun	Thymic iNKT single cell analyses unmask the common developmental program of Mouse innate T cells	"GSE152786, GSE160518"
Mouse	Parathyroid	"Gcm2, Ccl21a"	Parathyroid	Tissue	Thymocyte	31792212	Nat Commun	Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth	GSE131368
Mouse	Thymocytes	Cd3e	Thymocytes	Tissue	Thymocyte	31792212	Nat Commun	Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth	GSE131368
Mouse	Thyroid	Nkx2-1	Thyroid	Tissue	Thymocyte	31792212	Nat Commun	Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth	GSE131368
Mouse	Epithelial cells	"Itga6, Aire, Pigr, Il25, Ly6a, H2-aa, Ly6d, L1cam"	Medullary thymic Epithelial cells (mTEC)	Tissue	Thymocyte	31792212	Nat Commun	Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth	GSE131368
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Thymocyte	30643267	Nat Immunol	Thymic regulatory T cells arise via two distinct developmental programs.	GSE123067
Mouse	Epithelial cells	"Plet1, Cldn3, Cldn4"	TEC (thymic Epithelial cells) progenitors	Tissue	Thymocyte	31792212	Nat Commun	Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth	GSE131368
Mouse	Dn cells	"Il2ra, Hes1"	Dn cells	Tissue	Thymus	32358021	J Immunol	UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression	NA
Mouse	Dp cells	"Cd4, Cd8a"	Dp cells	Tissue	Thymus	32358021	J Immunol	UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression	NA
Mouse	T cells	"Ccr7, Itm2a"	Mature T cells	Tissue	Thymus	32358021	J Immunol	UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression	NA
Mouse	Thymocytes	CD4SP	Thymocytes	Tissue	Thymus	31434685	J Exp Med	IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus.	GSE134902
Mouse	T cells	"Kit, CD44"	Early T cell progenitors	Tissue	Thymus	31629685	Cell Syst	Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development	GSE130812 and GSE 137165
Mouse	T cells	"Cd163l1, Sox13"	Gamma delta T cells	Tissue	Thymus	32358021	J Immunol	UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression	NA
Mouse	Granulocytes	Elane	Granulocytes	Tissue	Thymus	31629685	Cell Syst	Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development	GSE130812 and GSE 137165
Mouse	Natural killer (NK) cells	Klrd1	Natural killer (NK) cells	Tissue	Thymus	31629685	Cell Syst	Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development	GSE130812 and GSE 137165
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Thymus	31434685	J Exp Med	IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus.	GSE134902
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Thymus	31434685	J Exp Med	IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus.	GSE134902
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Thymus	31434685	J Exp Med	IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus.	GSE134902
Mouse	T cells	Foxp3	Regulatory T cells (Treg)	Tissue	Thymus	31434685	J Exp Med	IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus.	GSE134902
Mouse	T cells	"Notch1, Gata3, Tcf7"	T cells	Tissue	Thymus	31629685	Cell Syst	Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development	GSE130812 and GSE 137165
Mouse	Epithelial cells	"CD45_, EpCAM"	Thymic epithelial cells	Tissue	Thymus	32709894	Nat Commun	Differential expression of tissue-restricted antigens among mTEC is associated with distinct autoreactive T cell fates	GSE153288
Mouse	Taste receptor cells	"Krt8, Krt19, Tas1r1, Tas1r2, Tas1r3, P2rx7"	Taste receptor cells	Tissue	Tongue	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Dendritic cells	"HLA-DR, CD11c"	Conventional dendritic cells	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"CCR7, LAMP3, CCL19, MARCKSL1, CD83, IDO1."	DC activation genes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"CD1C, FCER1A, CLEC10A."	CDC2	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"LGMN, CTSB, CD14, APOE, MARCO, CD163, FCGR3A, S100A8, MAFB."	Dendritic cells	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"RAB32, CLEC9A, IRF8, C1orf54, IDO1."	CDC1 genes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"LTB, PRDM16, LST1, RUNX3, CD164."	Progenitors or cDC development	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Dendritic cells	"PCLAF, STMN1, MKI67, TOP2A, CDK1."	Dendritic cells	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Myeloid cells	"FCN1, S100A9, VCAN, S100A8, MAFB"	Monocyte and macrophage-related genes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Monocytes	"CTSS, FCN1, S100A9, LYZ, VCAN."	Monocytes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Macrophages	"HLA-DR, CD11c, CD16"	Macrophages	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Macrophages	"LGMN, CTSB, CD14, APOE, C1QB, MARCO, CD163, FCGR3A."	Macrophage genes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Macrophages	"LGMN, CTSB, CD14, APOE, C1QB, MARCO, CD163, FCGR3A."	Macrophage genes	Tissue	Tonsil	29967419	Nat Commun	Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway	NA
Mouse	Endothelial cells	Pecam1	Endothelial cells	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	"Epcam, Cdh1, Krt15, Krt14"	Basal	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	"Epcam, Cdh1, Scgb1a1"	Secretory	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Epithelial cells	"Epcam, Cdh1, Foxj1"	Ciliated	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Immune cells	Ptprc	Immune cells	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Mesenchymal cells	Pdgfrb	Mesenchymal cells	Tissue	Trachea	30283141	Nature	Single-cell transcriptomics of 20 Mouse organs creates a Tabula Muris	GSE109774
Mouse	Endothelial cells	"Emcn, Ecscr, Cdh5, Igfbp7"	Endothelial cells	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	Endothelial cells	"Emcn, Ecscr, Cdh5, Igfbp7"	Endothelial cells	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	Neural cells	"Nefl, Nefm, Snap25, Tubb3"	Neurons	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	Neural cells	"Nefl, Nefm, Snap25, Tubb3"	Neurons	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	Glial cells	"Apoe, Fabp7, Dbi, Plp1"	Satellite glial cells	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	Glial cells	"Apoe, Fabp7, Dbi, Plp1"	Satellite glial cells	Tissue	Vagal Sensory Neurons	31730854	CELL	Genetic Identification of Vagal Sensory Neurons That Control Feeding	NA
Mouse	B cells	CD19	B cells	Tissue	Vaginal tissue and spleen	31189952	Nature	Migrant memory B cells secrete luminal antibody in the vagina	PRJNA524497
Mouse	Plasma cells	CD138	Plasma cells	Tissue	Vaginal tissue and spleen	31189952	Nature	Migrant memory B cells secrete luminal antibody in the vagina	PRJNA524497
Mouse	Plasmablasts	"CD138, CD19"	Plasmablasts	Tissue	Vaginal tissue and spleen	31189952	Nature	Migrant memory B cells secrete luminal antibody in the vagina	PRJNA524497
Mouse	T cells	"CD4, Foxp3, CD49b"	A short-lived effector Treg cell subset	Tissue	"Vasculature, skin"	30355617	J Exp Med	CD49b defines functionally mature Treg cells that survey skin and vascular tissues.	GSE121034
Mouse	Late activated nscs	Cdk1	Late activated nscs	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Quiescent nscs	Nltsr2	Quiescent nscs	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Microglia cells	Cx3cr1	Microglia cells	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Oligodendrocytes	Sox10	Oligodendrocytes precursors	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Ependymal cells	"Acta2, Foxj1"	Ependymal cells	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Neural cells	Thbs4	Activated neural stem cells	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Neuroblasts	Dcx	Neuroblasts	Tissue	Ventricle	29727663	Cell	Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.	GSE100320
Mouse	Fibroblasts-like cells	Pdgfra	Fibroblasts-like cells	Tissue	Vessel	30962620	Nature Methods	Evaluating measures of association for single-cell transcriptomics	"GSE84133, GSE81547, GSE81608, GSE85241"
Mouse	Enterocytes	"Npc1l1, Apoc3, Slc6a19, Lct"	Enterocytes	Tissue	Villus	30988513	Nat Genet	A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity	GSE112946
Mouse	Goblet cells	"Spdef, Atoh1, Muc2, Tff3"	Goblet cells	Tissue	Villus	30988513	Nat Genet	A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity	GSE112946
Mouse	Adipocytes	Sca1	Adipose progenitors	Tissue	Visceral Adipose progenitor cells	31767614	Life Science Alliance	Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling	NA
Mouse	Immature	"Clic1, Vamp8"	Immature	Tissue	Visual cortex	31027966	Neuron	Neocortical Projection Neurons Instruct Inhibitory Interneuron Circuit Development in a Lineage-Dependent Manner	GSE127724
Mouse	Astrocytes	Aqp4	Astrocytes	Tissue	Visual cortex	31027966	Neuron	Neocortical Projection Neurons Instruct Inhibitory Interneuron Circuit Development in a Lineage-Dependent Manner	GSE127724
Mouse	Neural cells	Slc17a7	Glutamatergic neurons	Tissue	Visual cortex	31027966	Neuron	Neocortical Projection Neurons Instruct Inhibitory Interneuron Circuit Development in a Lineage-Dependent Manner	GSE127724
Mouse	Neural cells	"Vip, Calb2, Chat, Reln, Ndnf, Npy, Lamp5, Nos1, Cck, Sst"	Interneurons	Tissue	Visual cortex	31027966	Neuron	Neocortical Projection Neurons Instruct Inhibitory Interneuron Circuit Development in a Lineage-Dependent Manner	GSE127724
Mouse	Oligodendrocytes	"Mbp, Olig1"	Oligodendrocytes	Tissue	Visual cortex	31027966	Neuron	Neocortical Projection Neurons Instruct Inhibitory Interneuron Circuit Development in a Lineage-Dependent Manner	GSE127724
Mouse	Definitive erythroid cells	"Gm15915, Ccl17, Muc13, Gdf3"	Definitive erythroid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Emp	"Spi1, Bcl11a, Myb, Tal1, Gata2"	Emp	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Emps	"cKit, Itga2b, Cd34, Spi1"	Emps	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Erythroid cells	"Epor, Hba-x, Gm15915, Ccl17, Muc13"	Erythroid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Primitive and definitive erythroid cells	"Gata1, Klf1, EpoR"	Primitive and definitive erythroid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Erythroid cells	"Hbb-y, Hba-x, Hbb-bh1"	Primitive erythroid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Pericytes	"Desmin, Hand1, Acta2, Tbx20, CD248"	Pericytes and smooth muscle cell	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Endothelial cells	"Kdr, Cdh5, Pecam1"	Endothelial cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Myeloid cells	"Trem2, Emr1, Cx3cr1, Csf1r"	Myeloid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Myeloid cells	"P2ry6, Fcgr1, CD86, Irf8, CD68"	Myeloid cells	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381
Mouse	Muscle cells	"Hand1, Hand2, Tbx20"	Pericytes and smooth muscle cells.	Tissue	Yolk sac	33207205	Cell Rep	Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors	GSE159381