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893
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659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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2339
datasets
CELLxGENE
4,992 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Erythroid lineage cell
+7
Erythroid lineage cell
Liver
Liver
16th week post-fertilization stage
16th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Erythroid lineage cell
Hepatocyte
Double negative thymocyte
Megakaryocyte
Vascular associated smooth muscle cell
Epithelial cell
Megakaryocyte progenitor cell
Mesothelial cell
Tissue
Liver
Developmental stage
16th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Human Cell Atlas Developmental:fetal-immune
Teichmann lab
UCSC Cell Browser:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
Github:Teichlab/Pan_fetal_immune
BroadInstitute Single-Cell Portal:SCP1843
CELLxGENE
4,992 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+4
Hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
Prime adult stage
Primary sclerosing cholangitis
Primary sclerosing cholangitis
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Centrilobular region hepatocyte
Intrahepatic cholangiocyte
Periportal region hepatocyte
Blood cell
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Disease
Primary sclerosing cholangitis
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
CELLxGENE
4,992 cells
•
Pranzatelli et al., 2024
GZMK+CD8+ T cells Target A Specific Acinar Cell Type in Sjögren’s Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Iga plasma cell
+4
Iga plasma cell
Labial gland
Labial gland
48-year-old stage
+1
48-year-old stage
Sjogren syndrome
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Iga plasma cell
Cd4-positive, alpha-beta t cell
Endothelial cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
48-year-old stage
40-year-old stage
Disease
Sjogren syndrome
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac muscle myoblast
+7
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
43-year-old stage
43-year-old stage
Myocardial infarction
Myocardial infarction
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Neuronal receptor cell
Pericyte
Cardiac endothelial cell
Lymphoid lineage restricted progenitor cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Tissue
Heart left ventricle
Developmental stage
43-year-old stage
Disease
Myocardial infarction
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6580069#.YvQwROzMI1w
Zenodo record:6578617#.YvQwQuzMI1w
CELLxGENE
4,992 cells
•
Li et al., 2022
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+23
Natural killer cell
Kidney
Kidney
Sixth decade stage
Sixth decade stage
Nonpapillary renal cell carcinoma
Nonpapillary renal cell carcinoma
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney loop of henle thick ascending limb epithelial cell
B cell
Naive b cell
Podocyte
Pericyte
Iga plasma cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Classical monocyte
Cd4-positive, alpha-beta t cell
Kidney collecting duct principal cell
Macrophage
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Cd8-positive, alpha-beta t cell
Igg plasma cell
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Mast cell
Epithelial cell of proximal tubule segment 3
Tissue
Kidney
Developmental stage
Sixth decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
DOI:10.17632/g67bkbnhhg.1
EGA dataset:EGAD00001008030
EGA dataset:EGAD00001008781
Github:ThomasJamesMitchell/deSCeRNAMut
Github:ruoyan-li/RCC-spatial-mapping
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
Sanger Institute Project:microenvironment-of-kidney-cancer
CELLxGENE
4,992 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Mammary gland epithelial cell
+7
Mammary gland epithelial cell
Breast
Breast
Prime adult stage
Prime adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Mammary gland epithelial cell
Adipocyte of breast
B cell
Pericyte
Endothelial cell of lymphatic vessel
Endothelial cell of vascular tree
Luminal epithelial cell of mammary gland
Fibroblast
Tissue
Breast
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
GEO series:GSE195665
CELLxGENE
4,992 cells
•
Pranzatelli et al., 2024
GZMK+CD8+ T cells Target A Specific Acinar Cell Type in Sjögren’s Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+7
Dendritic cell
Labial gland
Labial gland
64-year-old stage
+1
64-year-old stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
Iga plasma cell
Duct epithelial cell
Cd4-positive, alpha-beta t cell
Macrophage
Endothelial cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
64-year-old stage
56-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
CELLxGENE
4,992 cells
•
Ganier et al., 2024
Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma
Explore
h5ad
Homo sapiens
Homo sapiens
Basal cell of epidermis
+6
Basal cell of epidermis
Nose skin
Nose skin
77-year-old stage
77-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Basal cell of epidermis
Cell of skeletal muscle
Pericyte
Endothelial cell of vascular tree
Suprabasal keratinocyte
Chondrocyte
Fibroblast
Tissue
Nose skin
Developmental stage
77-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
spatial-skin-atlas.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
ArrayExpress BioStudies:E-MTAB-13085
CELLxGENE
4,992 cells
•
Valdeolivas et al., 2024
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
Explore
h5ad
Homo sapiens
Homo sapiens
Goblet cell
+14
Goblet cell
Rectum
Rectum
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Goblet cell
Regulatory t cell
B cell
Enterocyte
Pericyte
Iga plasma cell
Malignant cell
Smooth muscle cell
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Endothelial tip cell
Inflammatory macrophage
Transit amplifying cell of colon
Endothelial stalk cell
Tissue
Rectum
Developmental stage
Eighth decade stage
Disease
Colorectal cancer
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:alberto-valdeolivas/ST_CRC_CMS
Zenodo record:7760264
Zenodo record:7744244
CELLxGENE
4,992 cells
•
Ganier et al., 2024
Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+9
Schwann cell
Skin of breast
Skin of breast
42-year-old stage
42-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Basal cell of epidermis
Pericyte
Endothelial cell of lymphatic vessel
Smooth muscle cell
Macrophage
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Tissue
Skin of breast
Developmental stage
42-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
spatial-skin-atlas.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-13085
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Naive thymus-derived cd4-positive, alpha-beta t cell
+12
Naive thymus-derived cd4-positive, alpha-beta t cell
Interventricular septum
Interventricular septum
Fifth decade stage
Fifth decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Naive thymus-derived cd4-positive, alpha-beta t cell
Innate lymphoid cell
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Pericyte
Monocyte
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Vein endothelial cell
Mast cell
Tissue
Interventricular septum
Developmental stage
Fifth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Hepatocyte
+16
Hepatocyte
Liver
Liver
Young adult stage
Young adult stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Hepatocyte
Hepatic stellate cell
Endothelial cell of hepatic sinusoid
Peritoneal macrophage
Cholangiocyte
B cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Neutrophil
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Intermediate monocyte
Erythrocyte
Endothelial cell of pericentral hepatic sinusoid
Vascular associated smooth muscle cell
Hematopoietic stem cell
Fibroblast
Tissue
Liver
Developmental stage
Young adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
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