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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
•
Valdeolivas et al., 2024
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
Explore
h5ad
Homo sapiens
Homo sapiens
Regulatory t cell
+13
Regulatory t cell
Caecum
Caecum
Ninth decade stage
Ninth decade stage
Colorectal cancer
Colorectal cancer
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Regulatory t cell
B cell
Enterocyte
Pericyte
Malignant cell
Smooth muscle cell
Myofibroblast cell
Macrophage
Cd8-positive, alpha-beta t cell
Endothelial tip cell
Inflammatory macrophage
Endothelial cell
Mast cell
Endothelial stalk cell
Tissue
Caecum
Developmental stage
Ninth decade stage
Disease
Colorectal cancer
Sex
Male
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
•
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
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
T cell
Macrophage
Endothelial cell
Epithelial cell
Fibroblast
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
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
•
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
B cell
Malignant cell
Epithelial cell
Myeloid cell
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
•
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
Memory b cell
Neutrophil
Transit amplifying cell
Myofibroblast cell
Stem cell
Group 3 innate lymphoid cell
Enteric neuron
Germinal center b cell
Epithelial 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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+5
Schwann 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
Schwann cell
T cell
Pericyte
Endothelial cell
Epithelial cell
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
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE206710
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
+20
Goblet cell
Rectum
Rectum
Sixth decade stage
Sixth 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
Iga plasma cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Malignant cell
Smooth muscle cell
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Endothelial tip cell
Stromal cell
Transit amplifying cell of colon
Enteroglial cell
Mast cell
Endothelial stalk cell
Tissue
Rectum
Developmental stage
Sixth decade stage
Disease
Colorectal cancer
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:alberto-valdeolivas/ST_CRC_CMS
Zenodo record:7760264
Zenodo record:7744244
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
Schwann cell
+7
Schwann cell
Skin of cheek
Skin of cheek
76-year-old stage
76-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Basal cell of epidermis
Pericyte
Endothelial cell of lymphatic vessel
Macrophage
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Tissue
Skin of cheek
Developmental stage
76-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
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+18
Natural killer cell
Breast
Breast
88-year-old stage
88-year-old stage
Invasive ductal breast carcinoma
Invasive ductal breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Myoepithelial cell
Dendritic cell
T cell
Naive b cell
Memory b cell
Endothelial cell of lymphatic vessel
Monocyte
Malignant cell
Mature nk t cell
Perivascular cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Luminal epithelial cell of mammary gland
Endothelial cell
Plasmablast
Fibroblast
Myeloid cell
Tissue
Breast
Developmental stage
88-year-old stage
Disease
Invasive ductal 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
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
+7
Dendritic cell
Labial gland
Labial gland
41-year-old stage
41-year-old stage
Immune system disorder
+1
Immune system disorder
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
Iga plasma cell
Duct epithelial cell
Cd4-positive, alpha-beta t cell
Endothelial cell
Ionocyte
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
41-year-old stage
Disease
Immune system disorder
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
+15
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
Myofibroblast cell
Macrophage
Megakaryocyte
Vascular associated smooth muscle cell
Cycling dendritic cell
Mature b cell
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
Teichmann lab
UCSC Cell Browser:fetal-immune
Human Cell Atlas Developmental:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
BroadInstitute Single-Cell Portal:SCP1843
ArrayExpress BioStudies:E-MTAB-11341
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Plasmacytoid dendritic cell
+19
Plasmacytoid dendritic cell
Liver
Liver
10-month-old stage
10-month-old stage
Metabolic dysfunction-associated steatotic liver disease
Metabolic dysfunction-associated steatotic liver disease
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Plasmacytoid dendritic cell
Hepatocyte
Hepatic stellate cell
Innate lymphoid cell
Endothelial cell of hepatic sinusoid
Peritoneal macrophage
Cholangiocyte
B cell
Conventional dendritic cell
Neutrophil
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Macrophage
Intermediate monocyte
Erythrocyte
Endothelial cell of pericentral hepatic sinusoid
Basophil
Fibroblast
Cytotoxic t cell
Mesothelial cell
Tissue
Liver
Developmental stage
10-month-old stage
Disease
Metabolic dysfunction-associated steatotic liver disease
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
•
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
B cell
Malignant cell
Perivascular cell
Endothelial cell
Epithelial cell
Fibroblast
Myeloid cell
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
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