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Cell
893
Nucleus
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
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Intestine goblet cell
+18
Intestine goblet cell
Ileum
Ileum
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Intestine goblet cell
Motor neuron
Leukocyte
Intestinal crypt stem cell of large intestine
Progenitor cell
Enterocyte
Gut endothelial cell
Pericyte
Secretory cell
Intestinal crypt stem cell of small intestine
Monocyte
Neuroendocrine cell
Myofibroblast cell
Group 3 innate lymphoid cell
Interstitial cell of cajal
Enteric smooth muscle cell
Interneuron
Gut absorptive cell
Fibroblast
Tissue
Ileum
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158702
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
Endothelial cell of artery
+15
Endothelial cell of artery
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
Endothelial cell of artery
Epithelial cell of lung
Endothelial cell of lymphatic vessel
Fibroblast of lung
Myofibroblast cell
Tracheobronchial smooth muscle cell
Cd8-positive, alpha-beta t cell
Respiratory tract epithelial cell
Erythrocyte
Megakaryocyte
Vascular associated smooth muscle cell
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary neuroendocrine cell
Pulmonary interstitial fibroblast
Mesothelial 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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of artery
+8
Endothelial cell of artery
Apex of heart
Apex of heart
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
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Pericyte
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Vein endothelial cell
Cd16-positive, cd56-dim natural killer cell, human
Tissue
Apex of heart
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
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
Natural killer cell
+18
Natural killer cell
Breast
Breast
54-year-old stage
54-year-old stage
Invasive ductal breast carcinoma
Invasive ductal breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Myoepithelial cell
Dendritic cell
T cell
Naive b cell
Memory b cell
Endothelial cell of lymphatic vessel
Monocyte
Malignant cell
Mature nk t cell
Perivascular cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Luminal epithelial cell of mammary gland
Endothelial cell
Plasmablast
Fibroblast
Myeloid cell
Tissue
Breast
Developmental stage
54-year-old stage
Disease
Invasive ductal breast carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
EGA Study:EGAS00001005173
Zenodo record:4739739
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
+3
Hepatocyte
Capsule of liver
Capsule of 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
Erythrocyte
Fibroblast
Mesothelial cell
Tissue
Capsule of 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
•
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
+13
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney
Kidney
Sixth decade stage
Sixth 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
Pericyte
Iga plasma cell
Conventional dendritic cell
Epithelial cell of proximal tubule
Macrophage
Cd8-positive, alpha-beta t cell
Endothelial cell
Mhc-ii-positive classical monocyte
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Epithelial cell of proximal tubule segment 3
Tissue
Kidney
Developmental stage
Sixth 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
•
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
+8
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
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
Github:dpeerlab/Treg_depletion_reproducibility
dbGaP Study:phs002371
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
Plasmacytoid dendritic cell
+10
Plasmacytoid dendritic cell
Skin of back
Skin of back
60-year-old stage
60-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic 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
Mast cell
Tissue
Skin of back
Developmental stage
60-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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+10
Regular atrial cardiac myocyte
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
Regular atrial cardiac myocyte
Endothelial cell of artery
Glial cell
Neutrophil
Monocyte
Smooth muscle cell
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Endocardial cell
Vein endothelial cell
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
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
Schwann cell
+7
Schwann cell
Thymus
Thymus
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Dendritic cell
T cell
B cell
Pericyte
Endothelial cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
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
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
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
+26
Cd14-low, cd16-positive monocyte
Sinoatrial node
Sinoatrial node
Third decade stage
Third 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
Naive thymus-derived cd4-positive, alpha-beta t cell
Regular atrial cardiac myocyte
B cell
Endothelial cell of artery
Glial cell
Pericyte
Endothelial cell of lymphatic vessel
Neutrophil
Monocyte
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Cd16-negative, cd56-bright natural killer cell, human
Endothelial cell
Dendritic cell, human
Capillary endothelial cell
Endocardial cell
Activated cd4-positive, alpha-beta t cell
Vein endothelial cell
Plasma cell
Mast cell
Mucosal invariant t cell
Cardiac pacemaker cell of sinoatrial node
Tissue
Sinoatrial node
Developmental stage
Third 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
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
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
+11
Erythroid lineage cell
Thymus
Thymus
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
T cell
Mesenchymal cell
Myofibroblast cell
Macrophage
Alpha-beta t cell
Medullary thymic epithelial cell type 1
Vascular associated smooth muscle cell
Cd4-positive, alpha-beta thymocyte
Epithelial cell
Fibroblast
Double-positive, alpha-beta thymocyte
Tissue
Thymus
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
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
ArrayExpress BioStudies:E-MTAB-11343
BroadInstitute Single-Cell Portal:SCP1843
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