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896
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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
•
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
Natural killer cell
+9
Natural killer cell
Upper leg skin
Upper leg skin
53-year-old stage
53-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Smooth muscle cell
Endothelial cell of vascular tree
Basal cell of epidermis
Cell of skeletal muscle
Pericyte
Monocyte
Suprabasal keratinocyte
Fibroblast
Chondrocyte
Tissue
Upper leg skin
Developmental stage
53-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
Perivascular cell
+5
Perivascular cell
Breast
Breast
Adult stage
Adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
B cell
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE213688
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of hepatic sinusoid
+13
Endothelial cell of hepatic sinusoid
Liver
Liver
10-month-old stage
10-month-old stage
Metabolic dysfunction-associated steatotic liver disease
Metabolic dysfunction-associated steatotic liver disease
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Endothelial cell of hepatic sinusoid
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Kupffer cell
Plasmacytoid dendritic cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Cholangiocyte
Mesothelial cell
B cell
Peritoneal macrophage
Conventional dendritic cell
Fibroblast
Tissue
Liver
Developmental stage
10-month-old stage
Disease
Metabolic dysfunction-associated steatotic liver disease
Sex
Male
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
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Osteoblast
+20
Osteoblast
Hindlimb
Hindlimb
Carnegie stage 23
Carnegie stage 23
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Osteoblast
Muscle cell
Erythrocyte
Fibroblast of dermis
Peridermal cell
Hypertrophic chondrocyte
Tendon cell
Basal cell
Endothelial cell of artery
Schwann cell
Smooth muscle cell
Articular chondrocyte
Connective tissue cell
Primitive red blood cell
Macrophage
Vein endothelial cell
Pericyte
Reticulocyte
Fibroblast
Chondrocyte
Muscle fibroblast
Tissue
Hindlimb
Developmental stage
Carnegie stage 23
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Human Cell Atlas Developmental:embryonic-limb
ArrayExpress BioStudies:E-MTAB-10514
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-10367
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
Endothelial cell
+8
Endothelial cell
Labial gland
Labial gland
27-year-old stage
27-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Ionocyte
Myoepithelial cell
Duct epithelial cell
Acinar cell of salivary gland
Cd4-positive, alpha-beta t cell
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
27-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
•
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
T cell
+7
T 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
T cell
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
Malignant cell
B cell
Fibroblast
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
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+18
T cell
Breast
Breast
47-year-old stage
47-year-old stage
Invasive lobular breast carcinoma
Invasive lobular breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Endothelial cell of lymphatic vessel
Perivascular cell
Endothelial cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Luminal epithelial cell of mammary gland
Myoepithelial cell
Macrophage
Memory b cell
Myeloid cell
Plasmablast
Cd4-positive, alpha-beta t cell
Malignant cell
Monocyte
Naive b cell
Fibroblast
Dendritic cell
Tissue
Breast
Developmental stage
47-year-old stage
Disease
Invasive lobular 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
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Tracheobronchial smooth muscle cell
+15
Tracheobronchial smooth muscle cell
Lung
Lung
12th week post-fertilization stage
12th week post-fertilization stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Tracheobronchial smooth muscle cell
Endothelial cell of lymphatic vessel
Erythrocyte
Cd8-positive, alpha-beta t cell
Pulmonary neuroendocrine cell
Endothelial cell of artery
Respiratory tract epithelial cell
Pulmonary alveolar type 1 cell
Fibroblast of lung
Vein endothelial cell
Megakaryocyte
Mesothelial cell
Pulmonary interstitial fibroblast
Epithelial cell of lung
Vascular associated smooth muscle cell
Myofibroblast cell
Tissue
Lung
Developmental stage
12th week post-fertilization stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11265
CELLxGENE
4,992 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+15
T cell
Spleen
Spleen
18th week post-fertilization stage
18th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Erythroid lineage cell
Epithelial cell
Plasmacytoid dendritic cell
Megakaryocyte progenitor cell
Macrophage
Mature b cell
Common myeloid progenitor
Plasma cell
Megakaryocyte
Mesothelial cell
Cycling dendritic cell
Vascular associated smooth muscle cell
Myofibroblast cell
Conventional dendritic cell
Fibroblast
Tissue
Spleen
Developmental stage
18th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Teichmann lab
UCSC Cell Browser:fetal-immune
Human Cell Atlas Developmental:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
BroadInstitute Single-Cell Portal:SCP1843
ArrayExpress BioStudies:E-MTAB-11341
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
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
3-month-old stage
3-month-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Smooth muscle cell
Epithelial cell
Macrophage
Myelocyte
B cell
Dendritic cell
Tissue
Thymus
Developmental stage
3-month-old stage
Disease
Normal
Sex
Female
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
•
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
+16
Podocyte
Kidney
Kidney
Seventh decade stage
Seventh 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
Cd8-positive, alpha-beta t cell
Iga plasma cell
Epithelial cell of proximal tubule
Igg plasma cell
Epithelial cell of proximal tubule segment 1
Macrophage
Cd4-positive, alpha-beta t cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Collagen secreting cell
Kidney loop of henle ascending limb epithelial cell
Conventional dendritic cell
Fibroblast
Tissue
Kidney
Developmental stage
Seventh 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
•
Madissoon et al., 2022
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Explore
h5ad
Homo sapiens
Homo sapiens
Muscle cell
+24
Muscle cell
Bronchus
Bronchus
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
Muscle cell
Airway submucosal gland duct basal cell
Ciliated cell
Endothelial cell of lymphatic vessel
Lung secretory cell
Mast cell
Iga plasma cell
Blood vessel smooth muscle cell
Lung resident memory cd8-positive, alpha-beta t cell
Basal cell
Endothelial cell of artery
Smooth muscle cell of the pulmonary artery
Igg plasma cell
Bronchus fibroblast of lung
Lung macrophage
Regulatory t cell
Serous secreting cell of bronchus submucosal gland
Vein endothelial cell
Lung perichondrial fibroblast
Adventitial cell
Naive b cell
Fibroblast
Dendritic cell
Lung pericyte
Chondrocyte
Tissue
Bronchus
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ENA Project:PRJEB52292
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