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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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Most cells
Fewest cells
2339
datasets
CELLxGENE
4,992 cells
•
Glasner et al., 2023
Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies
Explore
h5ad
Mus musculus
Mus musculus
Alveolar macrophage
+9
Alveolar macrophage
Lung
Lung
5-month-old stage
5-month-old stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Alveolar macrophage
B cell
Ciliated cell
Pericyte
Myofibroblast cell
Macrophage
Capillary endothelial cell
Pulmonary alveolar type 1 cell
Epithelial cell
Fibroblast
Tissue
Lung
Developmental stage
5-month-old stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
Github:dpeerlab/Treg_depletion_reproducibility
CELLxGENE
4,992 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Neural cell
+4
Neural cell
Outflow tract myocardium
Outflow tract myocardium
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neural cell
Endothelial cell
Hematopoietic cell
Cardiac muscle cell
Cardiac mesenchymal cell
Tissue
Outflow tract myocardium
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ebi.ac.uk
ebi.ac.uk
ebi.ac.uk
ebi.ac.uk
DOI:10.7554/eLife.107748.1
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cd14-low, cd16-positive monocyte
+12
Cd14-low, cd16-positive monocyte
Atrioventricular node
Atrioventricular node
Eighth decade stage
Eighth decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cd14-low, cd16-positive monocyte
Regular atrial cardiac myocyte
Atrioventricular bundle cell
Regular ventricular cardiac myocyte
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Dendritic cell, human
Capillary endothelial cell
Vein endothelial cell
Tissue
Atrioventricular node
Developmental stage
Eighth 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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cd14-low, cd16-positive monocyte
+11
Cd14-low, cd16-positive monocyte
Atrioventricular node
Atrioventricular node
Eighth decade stage
Eighth decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cd14-low, cd16-positive monocyte
Regular atrial cardiac myocyte
Atrioventricular bundle cell
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Dendritic cell, human
Capillary endothelial cell
Tissue
Atrioventricular node
Developmental stage
Eighth 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-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
4,992 cells
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Breast
Breast
Breast carcinoma
Breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
B cell
Smooth muscle cell
Endothelial cell
Plasmablast
Epithelial cell
Myeloid cell
Tissue
Breast
Developmental stage
Disease
Breast carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
EGA Study:EGAS00001005173
Zenodo record:4739739
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Immature single positive thymocyte
+4
Immature single positive thymocyte
Thymus
Thymus
4-week-old stage
4-week-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Immature single positive thymocyte
Epithelial cell of thymus
Cd4-positive, alpha-beta thymocyte
Double-positive, alpha-beta thymocyte
Gamma-delta thymocyte
Tissue
Thymus
Developmental stage
4-week-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Plasmacytoid dendritic cell
+14
Plasmacytoid dendritic cell
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
Plasmacytoid dendritic cell
Hepatocyte
Hepatic stellate cell
Endothelial cell of hepatic sinusoid
Peritoneal macrophage
Cholangiocyte
B cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
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
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
Myoepithelial cell
+10
Myoepithelial cell
Labial gland
Labial gland
56-year-old stage
+1
56-year-old stage
Sjogren syndrome
+1
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Myoepithelial cell
Dendritic cell
Iga plasma cell
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Duct epithelial cell
Macrophage
Endothelial cell
Ionocyte
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
56-year-old stage
48-year-old stage
Disease
Sjogren syndrome
Normal
Sex
Female
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
Schwann cell
+6
Schwann cell
Inguinal part of abdomen
Inguinal part of abdomen
55-year-old stage
55-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Basal cell of epidermis
Pericyte
Smooth muscle cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Tissue
Inguinal part of abdomen
Developmental stage
55-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-13085
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
CELLxGENE
4,992 cells
•
Coutant et al., 2023
Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes
Explore
h5ad
Homo sapiens
Homo sapiens
B cell
+6
B cell
Breast
Breast
Adult stage
Adult stage
Triple-negative breast carcinoma
Triple-negative breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
B cell
Malignant cell
Perivascular cell
Endothelial cell
Epithelial cell
Fibroblast
Myeloid cell
Tissue
Breast
Developmental stage
Adult stage
Disease
Triple-negative breast carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE213688
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
Myoepithelial cell
+7
Myoepithelial cell
Labial gland
Labial gland
46-year-old stage
+1
46-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Myoepithelial cell
Dendritic cell
Iga plasma cell
Duct epithelial cell
Cd4-positive, alpha-beta t cell
Endothelial cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
46-year-old stage
55-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
Naive thymus-derived cd4-positive, alpha-beta t cell
+14
Naive thymus-derived cd4-positive, alpha-beta t cell
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
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney loop of henle thick ascending limb epithelial cell
Podocyte
Endothelial cell of lymphatic vessel
Classical monocyte
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Mhc-ii-positive classical monocyte
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Mast cell
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
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