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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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2346
datasets
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
+6
Endothelial cell
Labial gland
Labial gland
38-year-old stage
+1
38-year-old stage
Sjogren syndrome
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Ionocyte
Duct epithelial cell
Acinar cell of salivary gland
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
38-year-old stage
72-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
•
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
Ciliated cell
+8
Ciliated cell
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
Ciliated cell
Capillary endothelial cell
Epithelial cell
Pulmonary alveolar type 1 cell
Alveolar macrophage
B cell
Pericyte
Myofibroblast 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
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+7
Hepatocyte
Liver
Liver
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
Hepatocyte
Erythroid lineage cell
Epithelial cell
Megakaryocyte progenitor cell
Megakaryocyte
Mesothelial cell
Vascular associated smooth muscle cell
Double negative thymocyte
Tissue
Liver
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
ArrayExpress BioStudies:E-MTAB-11343
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
Github:Teichlab/Pan_fetal_immune
BroadInstitute Single-Cell Portal:SCP1843
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
+7
T 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
T cell
Endothelial cell
Smooth muscle cell
Epithelial cell
Macrophage
B cell
Fibroblast
Dendritic cell
Tissue
Thymus
Developmental stage
2-year-old stage
Disease
Normal
Sex
Male
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
•
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
+4
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
Endothelial cell
Myeloid cell
Malignant 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
•
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
+15
Endothelial cell of hepatic sinusoid
Liver
Liver
Young adult stage
Young adult stage
Normal
Normal
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
Endothelial cell of lymphatic vessel
Erythrocyte
Kupffer cell
Intermediate monocyte
Plasmacytoid dendritic cell
Hepatic stellate cell
Cholangiocyte
Hematopoietic stem cell
B cell
Vascular associated smooth muscle cell
Conventional dendritic cell
Fibroblast
Mononuclear phagocyte
Tissue
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
Podocyte
+17
Podocyte
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
Podocyte
Natural killer cell
Endothelial cell of lymphatic vessel
Endothelial cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Igg plasma cell
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney collecting duct principal cell
Kidney connecting tubule principal cell
Kidney loop of henle thick ascending limb epithelial 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
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
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
•
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
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
Smooth muscle cell
Macrophage
Glial cell
Vein endothelial cell
Cd14-positive monocyte
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
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-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
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
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
Epithelial cell
Macrophage
B cell
Tissue
Thymus
Developmental stage
3-month-old stage
Disease
Normal
Sex
Female
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
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Adipocyte of breast
+7
Adipocyte of breast
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
Adipocyte of breast
Endothelial cell of lymphatic vessel
Mammary gland epithelial cell
Luminal epithelial cell of mammary gland
Endothelial cell of vascular tree
B cell
Pericyte
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
•
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
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
T cell
Endothelial cell
Schwann cell
Smooth muscle cell
Epithelial cell
Pericyte
Fibroblast
Tissue
Thymus
Developmental stage
16th 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
•
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
+22
Muscle 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
Muscle cell
Airway submucosal gland duct basal cell
Ciliated cell
Lung secretory cell
Erythrocyte
Non-myelinating schwann cell
Iga plasma cell
Blood vessel smooth muscle cell
Basal cell
Igg plasma cell
Bronchus fibroblast of lung
Lung macrophage
Goblet cell
Memory b cell
Plasmablast
Serous secreting cell of bronchus submucosal gland
Alveolar macrophage
Vein endothelial cell
Respiratory tract suprabasal cell
Lung perichondrial fibroblast
Adventitial cell
Myofibroblast cell
Chondrocyte
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
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ArrayExpress BioStudies:E-MTAB-11640
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