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659
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43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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2339
datasets
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
+11
Pulmonary alveolar type 2 cell
Lung parenchyma
Lung parenchyma
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
Alveolar macrophage
Adventitial cell
Ciliated cell
Lung macrophage
Endothelial cell of lymphatic vessel
Muscle cell
Fibroblast of lung
Blood vessel smooth muscle cell
Blood vessel endothelial cell
Pulmonary alveolar type 1 cell
Plasmablast
Tissue
Lung parenchyma
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ArrayExpress BioStudies:E-MTAB-11640
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
2-year-old stage
2-year-old stage
Normal
Normal
Male
Male
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
2-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Bioimage Archive:S-BIAD1257
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Goblet cell
+11
Goblet cell
Colon
Colon
Prime adult stage
Prime adult stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Goblet cell
Enterocyte
Naive b cell
Endothelial cell of lymphatic vessel
Neutrophil
Transit amplifying cell
Myofibroblast cell
Macrophage
Stem cell
Germinal center b cell
Fibroblast
Cd103-positive dendritic cell
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Sanger Dataset:treg-gut-niches
ENA Project:PRJEB57700
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
+10
Endothelial cell of artery
Heart left ventricle
Heart left ventricle
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
Monocyte
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Capillary endothelial cell
Vein endothelial cell
Mast cell
Mesothelial cell
Tissue
Heart left ventricle
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
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac muscle myoblast
+8
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
44-year-old stage
44-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Neuronal receptor cell
Pericyte
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
44-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578617#.YvQwQuzMI1w
CELLxGENE
4,992 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Mammary gland epithelial cell
+7
Mammary gland epithelial cell
Breast
Breast
Prime adult stage
Prime adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Mammary gland epithelial cell
Adipocyte of breast
B cell
Pericyte
Endothelial cell of lymphatic vessel
Endothelial cell of vascular tree
Luminal epithelial cell of mammary gland
Fibroblast
Tissue
Breast
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
breastatlas.org
GEO series:GSE195665
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
Github:navinlabcode/HumanBreastCellAtlas
CELLxGENE
4,992 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Mammary gland epithelial cell
+7
Mammary gland epithelial 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
Mammary gland epithelial cell
Adipocyte of breast
B cell
Pericyte
Endothelial cell of lymphatic vessel
Endothelial cell of vascular tree
Luminal epithelial cell of mammary gland
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
GEO series:GSE195665
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
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac muscle myoblast
+8
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
60-year-old stage
60-year-old stage
Myocardial infarction
Myocardial infarction
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Neuronal receptor cell
Pericyte
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
60-year-old stage
Disease
Myocardial infarction
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
EGA Study:EGAS00001006330
Zenodo record:6578617#.YvQwQuzMI1w
Github:KramannLab/visium_heart
Zenodo record:6578047#.YvQwPezMI1w
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
+17
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
Podocyte
Iga plasma cell
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
Fibroblast
Kidney distal convoluted tubule epithelial cell
Kidney connecting tubule principal cell
Tissue
Kidney
Developmental stage
Sixth 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: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
•
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
+6
Myoepithelial cell
Labial gland
Labial gland
32-year-old stage
+1
32-year-old stage
Sjogren syndrome
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Myoepithelial cell
Iga plasma cell
Duct epithelial cell
Endothelial cell
Ionocyte
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
32-year-old stage
52-year-old stage
Disease
Sjogren syndrome
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
40-year-old stage
40-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
40-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578617#.YvQwQuzMI1w
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