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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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2339
datasets
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
Plasmacytoid dendritic cell
+9
Plasmacytoid dendritic 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
Plasmacytoid dendritic cell
Schwann cell
Natural killer cell
Basal cell of epidermis
Pericyte
Endothelial cell of lymphatic vessel
Smooth muscle cell
Endothelial cell of vascular tree
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cd14-low, cd16-positive monocyte
+28
Cd14-low, cd16-positive monocyte
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
Cd14-low, cd16-positive monocyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Innate lymphoid cell
Regular atrial cardiac myocyte
Effector memory cd8-positive, alpha-beta t cell
B cell
Endothelial cell of artery
Glial cell
Pericyte
Endothelial cell of lymphatic vessel
Neutrophil
Monocyte
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Macrophage
Cd8-positive, alpha-beta t cell
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Endothelial cell
Cd14-positive monocyte
Dendritic cell, human
Capillary endothelial cell
Endocardial cell
Activated cd4-positive, alpha-beta t cell
Vein endothelial cell
Mast cell
Cardiac pacemaker cell of sinoatrial node
Cd16-positive, cd56-dim natural killer cell, human
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-12916
ArrayExpress BioStudies:E-MTAB-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
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
Macrophage
Megakaryocyte
Vascular associated smooth muscle cell
Mature b cell
Epithelial cell
Fibroblast
Megakaryocyte progenitor cell
Mesothelial cell
Tissue
Spleen
Developmental stage
16th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Teichmann lab
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
Human Cell Atlas Developmental:fetal-immune
UCSC Cell Browser:fetal-immune
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
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
Plasmacytoid dendritic cell
+7
Plasmacytoid dendritic cell
Nose skin
Nose skin
82-year-old stage
82-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
Plasmacytoid dendritic cell
Natural killer cell
Basal cell of epidermis
Macrophage
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Tissue
Nose skin
Developmental stage
82-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
•
Li et al., 2022
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+17
Natural killer 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
Natural killer cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney loop of henle thick ascending limb epithelial cell
Podocyte
Pericyte
Iga plasma cell
Endothelial cell of lymphatic vessel
Classical monocyte
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Epithelial cell of proximal tubule segment 3
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
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
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Goblet cell
+9
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
Macrophage
Stem cell
Enteric neuron
Germinal center b cell
Fibroblast
Cd103-positive dendritic cell
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
•
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
+11
Schwann cell
Skin of temple
Skin of temple
68-year-old stage
68-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Natural killer cell
Basal cell of epidermis
Pericyte
Endothelial cell of lymphatic vessel
Smooth muscle cell
Macrophage
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Mast cell
Tissue
Skin of temple
Developmental stage
68-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
•
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 right ventricle
Heart right ventricle
Sixth decade stage
Sixth 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
Regular ventricular cardiac myocyte
Glial cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Endocardial cell
Vein endothelial cell
Tissue
Heart right ventricle
Developmental stage
Sixth 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
•
Li et al., 2022
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Epithelial cell of proximal tubule
+3
Epithelial cell of proximal tubule
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
Epithelial cell of proximal tubule
Endothelial cell
Epithelial cell of proximal tubule segment 1
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
•
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
+13
Naive thymus-derived cd4-positive, alpha-beta t cell
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
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney loop of henle thick ascending limb epithelial cell
Podocyte
Iga plasma cell
Conventional dendritic cell
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Cd8-positive, alpha-beta t cell
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Mhc-ii-positive classical monocyte
Collagen secreting 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:EGAD00001008030
Github:ThomasJamesMitchell/deSCeRNAMut
Sanger Institute Project:microenvironment-of-kidney-cancer
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
EGA dataset:EGAD00001008781
Github:ruoyan-li/RCC-spatial-mapping
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac muscle myoblast
+6
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
44-year-old stage
44-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Pericyte
Cardiac endothelial cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Mast cell
Tissue
Heart left ventricle
Developmental stage
44-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
EGA Study:EGAS00001006330
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
1
2
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157
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