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896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
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Most cells
Fewest cells
2346
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
T cell
+7
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
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
Malignant cell
B 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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+8
Endothelial cell of lymphatic vessel
Heart right ventricle
Heart right 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 lymphatic vessel
Endothelial cell of artery
Smooth muscle cell
Adipocyte
Vein endothelial cell
Pericyte
Mucosal invariant t cell
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart right 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-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
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
Natural killer cell
+9
Natural killer cell
Skin of abdomen
Skin of abdomen
47-year-old stage
47-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Endothelial cell of lymphatic vessel
Schwann cell
Smooth muscle cell
Plasmacytoid dendritic cell
Endothelial cell of vascular tree
Basal cell of epidermis
Pericyte
Suprabasal keratinocyte
Fibroblast
Tissue
Skin of abdomen
Developmental stage
47-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
•
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
+14
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
Plasmacytoid dendritic cell
Hepatic stellate cell
Cholangiocyte
Hematopoietic stem cell
B cell
Peritoneal macrophage
Vascular associated smooth muscle cell
Conventional dendritic cell
Fibroblast
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
•
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
Basal cell
+12
Basal cell
Skin of forehead
Skin of forehead
64-year-old stage
64-year-old stage
Basal cell carcinoma
Basal cell carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Basal cell
Schwann cell
Smooth muscle cell
Plasmacytoid dendritic cell
Endothelial cell of vascular tree
Basal cell of epidermis
Macrophage
Regulatory t cell
Plasma cell
Pericyte
Suprabasal keratinocyte
Conventional dendritic cell
Fibroblast
Tissue
Skin of forehead
Developmental stage
64-year-old stage
Disease
Basal cell carcinoma
Sex
Female
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
•
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
+16
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
Neutrophil
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Endothelial cell of lymphatic vessel
Erythrocyte
Kupffer cell
Intermediate monocyte
Hepatic stellate cell
Endothelial cell of pericentral hepatic sinusoid
Cholangiocyte
Hematopoietic stem cell
B cell
Peritoneal macrophage
Vascular associated smooth muscle cell
Conventional dendritic cell
Fibroblast
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
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+11
Neutrophil
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
Neutrophil
Germinal center b cell
Enteric neuron
Stem cell
Epithelial cell
Macrophage
Memory b cell
Glial cell
Enterocyte
Transit amplifying cell
Myofibroblast cell
Fibroblast
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
•
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
+8
Endothelial cell
Labial gland
Labial gland
52-year-old stage
+1
52-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
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Duct epithelial cell
Acinar cell of salivary gland
Cd4-positive, alpha-beta t cell
B cell
Fibroblast
Tissue
Labial gland
Developmental stage
52-year-old stage
55-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
•
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
Perivascular cell
+6
Perivascular 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
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
Malignant cell
B 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
•
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
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
GEO series:GSE195665
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+17
Neutrophil
Atrioventricular node
Atrioventricular 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
Neutrophil
Dendritic cell, human
Endothelial cell of lymphatic vessel
Endothelial cell
Mast cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Atrioventricular bundle cell
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Vein endothelial cell
Pericyte
Regular atrial cardiac myocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Atrioventricular 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-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
CELLxGENE
4,992 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+3
Endothelial cell
Outflow tract myocardium
Outflow tract myocardium
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Neural cell
Cardiac mesenchymal cell
Cardiac muscle cell
Tissue
Outflow tract myocardium
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ebi.ac.uk
ebi.ac.uk
ebi.ac.uk
ebi.ac.uk
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