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893
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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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+6
Dendritic 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
Dendritic cell
T cell
B cell
Smooth muscle cell
Macrophage
Epithelial cell
Myelocyte
Tissue
Thymus
Developmental stage
3-month-old stage
Disease
Normal
Sex
Female
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
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Decidual natural killer cell, human
+12
Decidual natural killer cell, human
Decidua basalis
Decidua basalis
Carnegie stage 18
Carnegie stage 18
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Decidual natural killer cell, human
B cell
Extravillous trophoblast
Endothelial cell of lymphatic vessel
Syncytiotrophoblast cell
Macrophage
Stromal cell
Trophoblast giant cell
Placental villous trophoblast
Endothelial cell of uterus
Embryonic fibroblast
Uterine smooth muscle cell
Epithelial cell
Tissue
Decidua basalis
Developmental stage
Carnegie stage 18
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:EGAD00001010038
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12698
EGA dataset:EGAD00001010017
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
+4
Erythroid lineage cell
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
Erythroid lineage cell
Hepatocyte
Double negative thymocyte
Vascular associated smooth muscle cell
Epithelial cell
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
+6
T cell
Thymus
Thymus
17th week post-fertilization stage
17th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
B cell
Pericyte
Macrophage
Endothelial cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
17th week post-fertilization stage
Disease
Normal
Sex
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
+8
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
Transit amplifying cell
Myofibroblast cell
Stem cell
Enteric neuron
Endothelial cell
Germinal center b 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
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
B cell
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
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
EGA dataset:EGAD00001015384
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Glial cell
+11
Glial 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
Glial cell
Enterocyte
Memory b cell
Neutrophil
Transit amplifying cell
Myofibroblast cell
Macrophage
Stem 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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cd14-low, cd16-positive monocyte
+15
Cd14-low, cd16-positive monocyte
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
Cd14-low, cd16-positive monocyte
Regular atrial cardiac myocyte
B cell
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Dendritic cell, human
Capillary endothelial cell
Vein endothelial cell
Cardiac pacemaker cell of sinoatrial node
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
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
+22
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
T follicular helper cell
Igg plasma cell
Endothelial tip cell
Inflammatory macrophage
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
•
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
+18
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney
Kidney
Seventh decade stage
Seventh 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
Non-classical monocyte
Podocyte
Iga plasma cell
Endothelial cell of lymphatic vessel
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Mhc-ii-positive classical monocyte
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Mast cell
Kidney connecting tubule principal cell
Tissue
Kidney
Developmental stage
Seventh 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
•
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
+18
Pulmonary alveolar type 2 cell
Bronchus
Bronchus
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
Pulmonary alveolar type 2 cell
Goblet cell
Respiratory tract suprabasal cell
Adventitial cell
Ciliated cell
Iga plasma cell
Non-myelinating schwann cell
Lung perichondrial fibroblast
Muscle cell
Lung pericyte
Lung secretory cell
Basal cell
Blood vessel smooth muscle cell
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Fibroblast
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
ArrayExpress BioStudies:E-MTAB-11640
Sanger Dataset:5locationslung
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
Bioimage Archive:S-BIAD570
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
+17
Pulmonary alveolar type 2 cell
Bronchus
Bronchus
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
Pulmonary alveolar type 2 cell
Goblet cell
Endothelial cell of artery
Adventitial cell
Ciliated cell
Iga plasma cell
Non-myelinating schwann cell
Muscle cell
Fibroblast of lung
Lung secretory cell
Basal cell
Blood vessel smooth muscle cell
Myelinating schwann cell
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Vein endothelial cell
Fibroblast
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
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