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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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Most cells
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2339
datasets
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
+12
Pulmonary alveolar type 2 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
Pulmonary alveolar type 2 cell
Alveolar macrophage
Adventitial cell
Lung macrophage
Endothelial cell of lymphatic vessel
Muscle cell
Fibroblast of lung
Blood vessel smooth muscle cell
Megakaryocyte
Blood vessel endothelial cell
Pulmonary artery endothelial cell
Pulmonary alveolar type 1 cell
Vein endothelial 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
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Plasmacytoid dendritic cell
+15
Plasmacytoid dendritic cell
Liver
Liver
Young adult stage
Young adult stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Plasmacytoid dendritic cell
Hepatocyte
Hepatic stellate cell
Endothelial cell of hepatic sinusoid
Cholangiocyte
B cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Mononuclear phagocyte
Intermediate monocyte
Erythrocyte
Vascular associated smooth muscle cell
Hematopoietic stem cell
Fibroblast
Tissue
Liver
Developmental stage
Young adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
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
Goblet cell
+25
Goblet cell
Trachea
Trachea
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
Goblet cell
Bronchus fibroblast of lung
Endothelial cell of artery
Respiratory tract suprabasal cell
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Lung perichondrial fibroblast
Lung pericyte
Lung secretory cell
Basal cell
Erythrocyte
Blood vessel smooth muscle cell
Igg plasma cell
Cd14-positive monocyte
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Lung interstitial macrophage
Plasmablast
Vein endothelial cell
Fibroblast
Airway submucosal gland duct basal cell
Tissue
Trachea
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ArrayExpress BioStudies:E-MTAB-11640
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
+7
Schwann cell
Skin of scalp
Skin of scalp
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
Smooth muscle cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Tissue
Skin of scalp
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
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
ArrayExpress BioStudies:E-MTAB-13084
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
Dendritic cell
+9
Dendritic cell
Labial gland
Labial gland
61-year-old stage
61-year-old stage
Sjogren syndrome
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
B cell
Iga plasma cell
Cd8-positive, alpha-beta cytotoxic t cell
Duct epithelial cell
Cd4-positive, alpha-beta t cell
Endothelial cell
Ionocyte
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
61-year-old stage
Disease
Sjogren syndrome
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Immature single positive thymocyte
+5
Immature single positive thymocyte
Thymus
Thymus
4-week-old stage
4-week-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Immature single positive thymocyte
Epithelial cell of thymus
Endothelial cell
Cd4-positive, alpha-beta thymocyte
Double-positive, alpha-beta thymocyte
Gamma-delta thymocyte
Tissue
Thymus
Developmental stage
4-week-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
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
+8
Hepatocyte
Liver
Liver
59-year-old stage
59-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Cholangiocyte
Neutrophil
Endothelial cell of periportal hepatic sinusoid
Macrophage
Vascular associated smooth muscle cell
Basophil
Fibroblast
Plasma cell
Tissue
Liver
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
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
+14
Schwann cell
Skin of external ear
Skin of external ear
90-year-old stage
90-year-old stage
Basal cell carcinoma
Basal cell carcinoma
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Natural killer cell
Regulatory t cell
Basal cell of epidermis
Pericyte
Endothelial cell of lymphatic vessel
Macrophage
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Cd8-positive, alpha-beta memory t cell, cd45ro-positive
Chondrocyte
Fibroblast
Plasma cell
Cytotoxic t cell
Tissue
Skin of external ear
Developmental stage
90-year-old stage
Disease
Basal cell carcinoma
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
+18
Cd14-low, cd16-positive monocyte
Interventricular septum
Interventricular septum
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
Cd14-low, cd16-positive monocyte
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Pericyte
Endothelial cell of lymphatic vessel
Neutrophil
Monocyte
Mature nk t cell
Smooth muscle cell
Macrophage
Cd8-positive, alpha-beta t cell
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Cd14-positive monocyte
Dendritic cell, human
Endocardial cell
Vein endothelial cell
Mucosal invariant t cell
Tissue
Interventricular septum
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-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
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
B cell
Smooth muscle cell
Macrophage
Endothelial cell
Epithelial 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:GSE271304
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE206710
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+15
Regular atrial cardiac myocyte
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
Regular atrial cardiac myocyte
Endothelial cell of artery
Glial cell
Endothelial cell of lymphatic vessel
Neutrophil
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Dendritic cell, human
Capillary endothelial cell
Endocardial cell
Vein endothelial cell
Mast cell
Cardiac pacemaker cell of sinoatrial node
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
•
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
47-year-old stage
47-year-old stage
Myocardial infarction
Myocardial infarction
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Neuronal receptor cell
Cardiac endothelial cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Mast cell
Tissue
Heart left ventricle
Developmental stage
47-year-old stage
Disease
Myocardial infarction
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578553#.YvQwPezMI1w
Github:saezlab/visium_heart
Zenodo record:6578617#.YvQwQuzMI1w
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