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Tissue
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Technology
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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
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+17
Plasmacytoid dendritic 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
Plasmacytoid dendritic cell
Erythroid lineage cell
T cell
Common myeloid progenitor
Conventional dendritic cell
Monocyte
Cd8-positive, alpha-beta thymocyte
Myofibroblast cell
Macrophage
Megakaryocyte
Vascular associated smooth muscle cell
Mature b cell
Cd4-positive, alpha-beta thymocyte
Epithelial cell
Fibroblast
Plasma cell
Megakaryocyte progenitor cell
Mesothelial cell
Tissue
Spleen
Developmental stage
18th 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
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
+7
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
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
•
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
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
Pericyte
Epithelial cell of proximal tubule
Macrophage
Endothelial cell
Epithelial cell of proximal tubule segment 1
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
Sanger Institute Project:microenvironment-of-kidney-cancer
Github:ruoyan-li/RCC-spatial-mapping
Github:ThomasJamesMitchell/deSCeRNAMut
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
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
+22
Pulmonary alveolar type 2 cell
Trachea
Trachea
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
Pulmonary alveolar type 2 cell
Goblet cell
Bronchus fibroblast of lung
Endothelial cell of artery
Respiratory tract suprabasal cell
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Lung perichondrial fibroblast
Lung pericyte
Lung secretory cell
Basal cell
Blood vessel smooth muscle cell
Igg plasma cell
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Lung interstitial macrophage
Vein endothelial cell
Fibroblast
Airway submucosal gland duct basal cell
Tissue
Trachea
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Sanger Dataset:5locationslung
Bioimage Archive:S-BIAD570
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
Natural killer cell
+25
Natural killer cell
Kidney
Kidney
Fifth decade stage
Fifth 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
Natural killer cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney loop of henle thick ascending limb epithelial cell
B cell
Naive b cell
Podocyte
Iga plasma cell
Classical monocyte
Activated type ii nk t cell
Cd4-positive, alpha-beta t cell
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Renal beta-intercalated cell
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Renal alpha-intercalated cell
Epithelial cell
Fibroblast
Kidney distal convoluted tubule epithelial cell
Epithelial cell of proximal tubule segment 3
Kidney connecting tubule principal cell
Tissue
Kidney
Developmental stage
Fifth decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
DOI:10.17632/g67bkbnhhg.1
EGA dataset:EGAD00001008781
Github:ThomasJamesMitchell/deSCeRNAMut
Github:ruoyan-li/RCC-spatial-mapping
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
EGA dataset:EGAD00001008030
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
+3
T 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
T cell
Pericyte
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
ccgg.ugent.be
Github:Teichlab/TissueTag
GEO series:GSE206710
Github:Teichlab/thymus_spatial_atlas/tree/main
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
Goblet cell
+16
Goblet cell
Right colon
Right colon
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Goblet cell
Regulatory t cell
B cell
Enterocyte
Pericyte
Conventional dendritic cell
Malignant cell
Smooth muscle cell
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Macrophage
Cd8-positive, alpha-beta t cell
Inflammatory macrophage
Stromal cell
Transit amplifying cell of colon
Endothelial cell
Endothelial stalk cell
Tissue
Right colon
Developmental stage
Eighth 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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+14
Regular atrial cardiac myocyte
Sinoatrial node
Sinoatrial node
Fifth decade stage
Fifth 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
Pericyte
Endothelial cell of lymphatic vessel
Neutrophil
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Endothelial cell
Endocardial cell
Vein endothelial cell
Mast cell
Cardiac pacemaker cell of sinoatrial node
Tissue
Sinoatrial node
Developmental stage
Fifth 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
Dendritic cell
+6
Dendritic cell
Thymus
Thymus
19th week post-fertilization stage
19th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
T cell
Pericyte
Granulocyte monocyte progenitor cell
Smooth muscle cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
19th week post-fertilization stage
Disease
Normal
Sex
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
•
Pranzatelli et al., 2024
GZMK+CD8+ T cells Target A Specific Acinar Cell Type in Sjögren’s Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+9
Dendritic cell
Labial gland
Labial gland
54-year-old stage
+1
54-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
B cell
Cd8-positive, alpha-beta regulatory t cell
Iga plasma cell
Smooth muscle cell
Duct epithelial cell
Cd4-positive, alpha-beta t cell
Endothelial cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
54-year-old stage
52-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
dbGaP Study:phs002446
Github:pranzatelli/scRNAseqNM2023
CELLxGENE
4,992 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+5
Hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
Prime adult stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
B cell
Centrilobular region hepatocyte
Endothelial cell
Periportal region hepatocyte
Blood cell
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE245620
GEO series:GSE247128
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
+7
Dendritic 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
Dendritic cell
T cell
B cell
Smooth muscle cell
Macrophage
Endothelial cell
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
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
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