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896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
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Most cells
Fewest cells
2346
datasets
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
Endothelial tip cell
+8
Endothelial tip cell
Sigmoid colon
Sigmoid colon
Seventh decade stage
Seventh decade stage
Colorectal cancer
Colorectal cancer
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial tip cell
Endothelial cell
Inflammatory macrophage
Smooth muscle cell
Macrophage
Endothelial stalk cell
Malignant cell
Pericyte
Myofibroblast cell
Tissue
Sigmoid colon
Developmental stage
Seventh decade stage
Disease
Colorectal cancer
Sex
Female
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
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+5
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
44-year-old stage
44-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Immature innate lymphoid cell
Neuronal receptor cell
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
44-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
CELLxGENE
4,992 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Thymus
Thymus
2-year-old stage
2-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Endothelial cell
Smooth muscle cell
Epithelial cell
Macrophage
B cell
Dendritic cell
Tissue
Thymus
Developmental stage
2-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE206710
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
+5
Iga plasma cell
Labial gland
Labial gland
58-year-old stage
58-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
Duct epithelial cell
Acinar cell of salivary gland
Cd4-positive, alpha-beta t cell
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
58-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 endothelial cell
+7
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
66-year-old stage
66-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Mast cell
Lymphoid lineage restricted progenitor cell
Immature innate lymphoid cell
Neuronal receptor cell
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
66-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+7
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
57-year-old stage
57-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Mast cell
Lymphoid lineage restricted progenitor cell
Immature innate lymphoid cell
Neuronal receptor cell
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
57-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578617#.YvQwQuzMI1w
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+6
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
47-year-old stage
47-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Mast cell
Immature innate lymphoid cell
Neuronal receptor cell
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
47-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+11
Hepatocyte
Liver
Liver
68-year-old stage
68-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Plasmacytoid dendritic cell
Hepatic stellate cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Cholangiocyte
Plasma cell
Vascular associated smooth muscle cell
Basophil
Conventional dendritic cell
Fibroblast
Non-classical monocyte
Tissue
Liver
Developmental stage
68-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
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
Podocyte
+14
Podocyte
Kidney
Kidney
Eighth decade stage
Eighth decade stage
Nonpapillary renal cell carcinoma
Nonpapillary renal cell carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Podocyte
Endothelial cell of lymphatic vessel
Endothelial cell
Mast cell
Classical monocyte
Epithelial cell of proximal tubule
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Mhc-ii-positive classical monocyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Collagen secreting cell
Kidney loop of henle ascending limb epithelial cell
Fibroblast
Tissue
Kidney
Developmental stage
Eighth decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Female
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
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Germinal center b cell
+8
Germinal center b cell
Colon
Colon
Prime adult stage
Prime adult stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Germinal center b cell
Endothelial cell
Enteric neuron
Stem cell
Goblet cell
Enterocyte
Transit amplifying cell
Myofibroblast cell
Fibroblast
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Sanger Dataset:treg-gut-niches
ENA Project:PRJEB57700
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+7
Cardiac endothelial cell
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 endothelial cell
Mast cell
Lymphoid lineage restricted progenitor cell
Immature innate lymphoid cell
Pericyte
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
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
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
EGA Study:EGAS00001006330
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endocardial cell
+12
Endocardial cell
Right cardiac atrium
Right cardiac atrium
Seventh decade stage
Seventh decade stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endocardial cell
Dendritic cell, human
Endothelial cell of artery
Smooth muscle cell of the pulmonary artery
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Plasma cell
Vein endothelial cell
Mesothelial cell
B cell
Regular atrial cardiac myocyte
Monocyte
Fibroblast of cardiac tissue
Tissue
Right cardiac atrium
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Male
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
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