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934
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679
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
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Most cells
Fewest cells
2515
datasets
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Germinal center b cell
+8
Germinal center b 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
Germinal center b cell
Enteric neuron
Stem cell
Macrophage
Memory b 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
treg-gut-niches.cellgeni.sanger.ac.uk
scRNA-seq, scTCR-seq and Visium data
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+9
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
Endothelial cell of lymphatic vessel
Enteric neuron
Stem cell
Enterocyte
Transit amplifying cell
Monocyte
Myofibroblast cell
Fibroblast
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
treg-gut-niches.cellgeni.sanger.ac.uk
scRNA-seq, scTCR-seq and Visium data
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
+12
Stromal cell
Decidua basalis
Decidua basalis
9th week post-fertilization stage
9th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Stromal cell
Endothelial cell of lymphatic vessel
Trophoblast giant cell
Extravillous trophoblast
Uterine smooth muscle cell
Epithelial cell
Decidual natural killer cell, human
Placental villous trophoblast
Macrophage
Endothelial cell of placenta
Embryonic fibroblast
Hofbauer cell
Syncytiotrophoblast cell
Tissue
Decidua basalis
Developmental stage
9th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Online web portal
scRNA-seq and snRNA-seq of primary tissue (E-MTAB-12421)
multiome snRNA-seq and snATAC-seq (E-MTAB-12595)
scRNA-seq and snRNA-seq of historical placental beds(EGAD00001010037)
multiome snRNA-seq and snATAC-seq of historical placental beds(EGAD00001010038)
scRNA-seq and snRNA-seq of TSCs(EGAD00001010017)
Image datasets
scRNA-seq and snucRNA-seq of human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs) (E-MTAB-12650)
Spatial transcriptomics of human implantation sites, placenta and decidua (E-MTAB-12698)
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
Endothelial cell of lymphatic vessel
Stem cell
Goblet cell
Macrophage
Cd103-positive dendritic cell
Enterocyte
Transit amplifying cell
Naive b cell
Myofibroblast cell
Fibroblast
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
treg-gut-niches.cellgeni.sanger.ac.uk
scRNA-seq, scTCR-seq and Visium data
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Germinal center b cell
+9
Germinal center b 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
Germinal center b cell
Enteric neuron
Stem cell
Goblet cell
Macrophage
Cd103-positive dendritic 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
treg-gut-niches.cellgeni.sanger.ac.uk
scRNA-seq, scTCR-seq and Visium data
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
+23
Podocyte
Kidney
Kidney
Sixth decade stage
Sixth 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
Podocyte
Natural killer cell
Endothelial cell of lymphatic vessel
Endothelial cell
Mast cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Classical monocyte
Igg plasma cell
Epithelial cell of proximal tubule segment 1
Macrophage
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Epithelial cell of proximal tubule segment 3
Cd4-positive, alpha-beta t cell
B cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Collagen secreting cell
Naive b 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
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
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
+14
Podocyte
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
Podocyte
Endothelial cell of lymphatic vessel
Endothelial cell
Mast cell
Classical monocyte
Epithelial cell of proximal tubule
Epithelial cell of proximal tubule segment 1
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
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
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
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
+3
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
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
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
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
+25
Podocyte
Kidney
Kidney
Fifth decade stage
Fifth 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
Podocyte
Natural killer cell
Renal beta-intercalated cell
Endothelial cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Activated type ii nk t cell
Classical monocyte
Epithelial cell of proximal tubule
Epithelial cell
Igg plasma cell
Epithelial cell of proximal tubule segment 1
Renal alpha-intercalated cell
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule principal cell
Kidney loop of henle thick ascending limb epithelial cell
Epithelial cell of proximal tubule segment 3
Cd4-positive, alpha-beta t cell
B cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Collagen secreting cell
Naive b cell
Kidney loop of henle ascending limb epithelial cell
Fibroblast
Tissue
Kidney
Developmental stage
Fifth decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
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
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
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
+18
Podocyte
Kidney
Kidney
Seventh decade stage
Seventh 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 of lymphatic vessel
Endothelial cell
Mast cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Epithelial cell of proximal tubule
Igg plasma cell
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Epithelial cell of proximal tubule segment 3
Cd4-positive, alpha-beta t cell
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
Seventh decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Single cell RNA sequencing and spatial transcriptomics data
Single cell RNA sequencing data (EGAD00001008030)
Spatial transcriptomic data (EGAD00001008781)
Code and pipeline for deSCeRNAmut
Online web portal
Analysis scripts
data.humancellatlas.org
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+11
Hepatocyte
Liver
Liver
59-year-old stage
59-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Kupffer cell
Macrophage
Cholangiocyte
Plasma cell
B cell
Vascular associated smooth muscle cell
Conventional dendritic cell
Fibroblast
Non-classical monocyte
Tissue
Liver
Developmental stage
59-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GSE192742
livercellatlas.org
explore.data.humancellatlas.org
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