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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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+10
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
Erythrocyte
Endothelial cell
Mast cell
Smooth muscle cell
Epithelial cell
Macrophage
B cell
Pericyte
Fibroblast
Dendritic cell
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
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
•
Madissoon et al., 2022
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Explore
h5ad
Homo sapiens
Homo sapiens
Muscle cell
+12
Muscle cell
Lung parenchyma
Lung parenchyma
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
Muscle cell
Blood vessel endothelial cell
Endothelial cell of lymphatic vessel
Blood vessel smooth muscle cell
Lung macrophage
Pulmonary alveolar type 1 cell
Fibroblast of lung
Alveolar macrophage
Vein endothelial cell
Megakaryocyte
Pulmonary artery endothelial cell
Adventitial cell
Pulmonary alveolar type 2 cell
Tissue
Lung parenchyma
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
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+11
Endothelial cell of lymphatic vessel
Apex of heart
Apex of heart
Fifth decade stage
Fifth decade stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Endothelial cell
Endothelial cell of artery
Capillary endothelial cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Vein endothelial cell
B cell
Pericyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Apex of heart
Developmental stage
Fifth 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
•
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
Carnegie stage 18
Carnegie stage 18
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
Endothelial cell of uterus
Placental villous trophoblast
Macrophage
Embryonic fibroblast
B cell
Syncytiotrophoblast 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
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010038
EGA dataset:EGAD00001010017
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12595
ArrayExpress BioStudies: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
Sanger Dataset:treg-gut-niches
ENA Project:PRJEB57700
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
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
Endothelial cell
Epithelial cell
B 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
•
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
+8
Endothelial cell
Labial gland
Labial gland
45-year-old stage
45-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
Endothelial cell
Iga plasma cell
Ionocyte
Igg plasma cell
Myoepithelial cell
Duct epithelial cell
Acinar cell of salivary gland
Cd8-positive, alpha-beta regulatory t cell
Fibroblast
Tissue
Labial gland
Developmental stage
45-year-old stage
Disease
Immune system disorder
Sjogren syndrome
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
Iga plasma cell
+4
Iga plasma cell
Labial gland
Labial gland
61-year-old stage
+1
61-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Iga plasma cell
Myoepithelial cell
Duct epithelial cell
Acinar cell of salivary gland
Fibroblast
Tissue
Labial gland
Developmental stage
61-year-old stage
62-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
CELLxGENE
4,992 cells
•
Glasner et al., 2023
Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies
Explore
h5ad
Mus musculus
Mus musculus
Ciliated cell
+9
Ciliated cell
Lung
Lung
5-month-old stage
5-month-old stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Ciliated cell
Capillary endothelial cell
Epithelial cell
Macrophage
Pulmonary alveolar type 1 cell
Alveolar macrophage
B cell
Pericyte
Myofibroblast cell
Fibroblast
Tissue
Lung
Developmental stage
5-month-old stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
humantumoratlas.org
Github:dpeerlab/Treg_depletion_reproducibility
dbGaP Study:phs002371
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
T cell
+18
T cell
Breast
Breast
49-year-old stage
49-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
T cell
Natural killer cell
Endothelial cell of lymphatic vessel
Perivascular cell
Endothelial cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Luminal epithelial cell of mammary gland
Myoepithelial cell
Macrophage
Memory b cell
Myeloid cell
Plasmablast
Cd4-positive, alpha-beta t cell
Malignant cell
Monocyte
Naive b cell
Fibroblast
Dendritic cell
Tissue
Breast
Developmental stage
49-year-old stage
Disease
Invasive ductal breast carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
Zenodo record:4739739
EGA Study:EGAS00001005173
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Adipocyte of epicardial fat of left ventricle
+9
Adipocyte of epicardial fat of left ventricle
Heart left ventricle
Heart left ventricle
44-year-old stage
44-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Adipocyte of epicardial fat of left ventricle
Cardiac endothelial cell
Mast cell
Lymphoid lineage restricted progenitor cell
Immature innate lymphoid cell
Neuronal receptor cell
Pericyte
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
44-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Github:KramannLab/visium_heart
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6580069#.YvQwROzMI1w
Zenodo record:6578617#.YvQwQuzMI1w
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