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Technology
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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
•
Valdeolivas et al., 2024
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial tip cell
+24
Endothelial tip cell
Rectosigmoid junction
Rectosigmoid junction
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial tip cell
Stromal cell
Natural killer cell
Endothelial cell of lymphatic vessel
Endothelial cell
Mast cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Inflammatory macrophage
Smooth muscle cell
Enteroglial cell
Igg plasma cell
Goblet cell
Transit amplifying cell of colon
Macrophage
Regulatory t cell
Endothelial stalk cell
Enterocyte
Cd4-positive, alpha-beta t cell
Malignant cell
T follicular helper cell
B cell
Pericyte
Myofibroblast cell
Conventional dendritic cell
Tissue
Rectosigmoid junction
Developmental stage
Eighth decade stage
Disease
Colorectal cancer
Sex
Male
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
•
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
5-month-old stage
5-month-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
Tissue
Thymus
Developmental stage
5-month-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:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE271304
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
+10
Endothelial cell
Labial gland
Labial gland
69-year-old stage
69-year-old stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Ionocyte
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
Dendritic cell
Tissue
Labial gland
Developmental stage
69-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
+13
Podocyte
Kidney
Kidney
Sixth decade stage
Sixth 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
Podocyte
Endothelial cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Epithelial cell of proximal tubule
Macrophage
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Mhc-ii-positive classical monocyte
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
Female
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac pacemaker cell of sinoatrial node
+26
Cardiac pacemaker cell of sinoatrial node
Sinoatrial node
Sinoatrial node
Fifth decade stage
Fifth decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac pacemaker cell of sinoatrial node
Neutrophil
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Activated cd4-positive, alpha-beta t cell
Endothelial cell
Mast cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Innate lymphoid cell
Glial cell
Vein endothelial cell
Cd14-positive monocyte
B cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Regular atrial cardiac myocyte
Monocyte
Fibroblast of cardiac tissue
Tissue
Sinoatrial node
Developmental stage
Fifth decade stage
Disease
Normal
Sex
Female
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
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Transit amplifying cell of small intestine
+24
Transit amplifying cell of small intestine
Colon
Colon
20th week post-fertilization stage
20th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Transit amplifying cell of small intestine
Intestine goblet cell
Intestinal crypt stem cell of large intestine
Secretory cell
Neuroendocrine cell
Interstitial cell of cajal
Erythroid lineage cell
Leukocyte
Gut absorptive cell
Inhibitory motor neuron
Precursor b cell
Enteroendocrine cell
Gut endothelial cell
Transit amplifying cell of colon
Macrophage
Enteric smooth muscle cell
Enterocyte
Motor neuron
Interneuron
Pericyte
Progenitor cell
Intestinal crypt stem cell of small intestine
Monocyte
Myofibroblast cell
Fibroblast
Tissue
Colon
Developmental stage
20th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158702
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac pacemaker cell of sinoatrial node
+25
Cardiac pacemaker cell of sinoatrial node
Sinoatrial node
Sinoatrial node
Third decade stage
Third decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac pacemaker cell of sinoatrial node
Neutrophil
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Activated cd4-positive, alpha-beta t cell
Endothelial cell
Mast cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Glial cell
Plasma cell
Vein endothelial cell
Cd14-positive monocyte
Cd14-low, cd16-positive monocyte
B cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Regular atrial cardiac myocyte
Monocyte
Fibroblast of cardiac tissue
Tissue
Sinoatrial node
Developmental stage
Third decade stage
Disease
Normal
Sex
Female
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
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+5
Endothelial cell
Thymus
Thymus
21-day-old stage
21-day-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Endothelial cell
Double-positive, alpha-beta thymocyte
Immature single positive thymocyte
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Cd4-positive, alpha-beta thymocyte
Epithelial cell of thymus
Tissue
Thymus
Developmental stage
21-day-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
CELLxGENE
4,992 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Erythroid lineage cell
+8
Erythroid lineage cell
Spleen
Spleen
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
Erythroid lineage cell
Epithelial cell
Megakaryocyte progenitor cell
Macrophage
Mature b cell
Megakaryocyte
Mesothelial cell
Vascular associated smooth muscle cell
Fibroblast
Tissue
Spleen
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
Github:Teichlab/Pan_fetal_immune
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
BroadInstitute Single-Cell Portal:SCP1843
DOI:10.1016/j.stem.2018.12.011
ArrayExpress BioStudies:E-MTAB-11341
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
Endothelial cell
+7
Endothelial 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
Endothelial cell
Epithelial cell of proximal tubule
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney loop of henle thick ascending limb epithelial cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
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
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Stromal cell
+9
Stromal cell
Decidua basalis
Decidua basalis
Carnegie stage 23
Carnegie stage 23
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Stromal cell
Extravillous trophoblast
Uterine smooth muscle cell
Epithelial cell
Decidual natural killer cell, human
Endothelial cell of uterus
Placental villous trophoblast
Endothelial cell of placenta
Hofbauer cell
Syncytiotrophoblast cell
Tissue
Decidua basalis
Developmental stage
Carnegie stage 23
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-12421
ArrayExpress BioStudies:E-MTAB-12595
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010017
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
EGA dataset:EGAD00001010038
ArrayExpress BioStudies:E-MTAB-12698
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell, human
+11
Dendritic cell, human
Atrioventricular node
Atrioventricular node
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
Dendritic cell, human
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Atrioventricular bundle cell
Macrophage
Glial cell
Cd14-low, cd16-positive monocyte
Regular atrial cardiac myocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Atrioventricular node
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
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
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