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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
•
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
+5
B 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
B cell
Perivascular cell
Endothelial cell
Epithelial cell
Fibroblast
Myeloid cell
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
•
Valdeolivas et al., 2024
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
Explore
h5ad
Homo sapiens
Homo sapiens
Enterocyte
+12
Enterocyte
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
Enterocyte
Pericyte
Malignant cell
Smooth muscle cell
Myofibroblast cell
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Inflammatory macrophage
Stromal cell
Enteroglial cell
Mast cell
Endothelial stalk cell
Tissue
Sigmoid colon
Developmental stage
Seventh decade stage
Disease
Colorectal cancer
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:7760264
Zenodo record:7744244
Github:alberto-valdeolivas/ST_CRC_CMS
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
Malignant cell
+2
Malignant 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
Malignant cell
Epithelial 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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+4
T cell
Thymus
Thymus
14-month-old stage
14-month-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
B cell
Macrophage
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
14-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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+5
Dendritic cell
Thymus
Thymus
6-month-old stage
6-month-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
T cell
B cell
Macrophage
Epithelial cell
Myelocyte
Tissue
Thymus
Developmental stage
6-month-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
EGA dataset:EGAD00001015384
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
Pulmonary alveolar type 2 cell
+26
Pulmonary alveolar type 2 cell
Bronchus
Bronchus
59-year-old stage
59-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Pulmonary alveolar type 2 cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Dendritic cell
Goblet cell
Respiratory tract suprabasal cell
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Endothelial cell of lymphatic vessel
Lung perichondrial fibroblast
Muscle cell
Fibroblast of lung
Neuroendocrine cell
Myofibroblast cell
Lung secretory cell
Basal cell
Blood vessel smooth muscle cell
Igg plasma cell
Cd14-positive monocyte
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Lung interstitial macrophage
Plasmablast
Vein endothelial cell
Mast cell
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
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
Natural killer cell
+17
Natural killer cell
Lung
Lung
17th week post-fertilization stage
17th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Pulmonary alveolar type 2 cell
Bronchus fibroblast of lung
Club cell
Lung multiciliated epithelial cell
Epithelial cell of lung
Neuron
Fibroblast of lung
Macrophage
Tracheobronchial smooth muscle cell
Respiratory tract epithelial cell
Erythrocyte
Vascular associated smooth muscle cell
Endothelial cell
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
17th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11265
Sanger Dataset:fetal-lung
genome.ucsc.edu
ArrayExpress BioStudies:E-MTAB-11266
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
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
+9
Cardiac muscle myoblast
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 muscle myoblast
Neuronal receptor cell
Pericyte
Adipocyte of epicardial fat of left ventricle
Cardiac endothelial cell
Lymphoid lineage restricted progenitor cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Mast cell
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
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
Github:KramannLab/visium_heart
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
Mus musculus
Mus musculus
Hepatocyte
+10
Hepatocyte
Liver
Liver
10-month-old stage
10-month-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Hepatocyte
Endothelial cell of hepatic sinusoid
Cholangiocyte
B cell
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Intermediate monocyte
Erythrocyte
Endothelial cell of pericentral hepatic sinusoid
Fibroblast
Mesothelial cell
Tissue
Liver
Developmental stage
10-month-old stage
Disease
Normal
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
•
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
+7
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
Male
Male
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
Kidney pelvis urothelial cell
Macrophage
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
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
EGA dataset:EGAD00001008030
EGA dataset:EGAD00001008781
Github:ThomasJamesMitchell/deSCeRNAMut
Github:ruoyan-li/RCC-spatial-mapping
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
DOI:10.17632/g67bkbnhhg.1
Sanger Institute Project:microenvironment-of-kidney-cancer
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
+2
T cell
Thymus
Thymus
18th week post-fertilization stage
18th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
18th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
EGA dataset:EGAD00001015384
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
+7
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
Fibroblast
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
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