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Technology
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Cell
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
•
Valdeolivas et al., 2024
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial tip cell
+13
Endothelial tip cell
Rectum
Rectum
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial tip cell
Stromal cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Inflammatory macrophage
Igg plasma cell
Goblet cell
T-helper 17 cell
Transit amplifying cell of colon
Regulatory t cell
Enterocyte
Cd4-positive, alpha-beta t cell
Malignant cell
B cell
Tissue
Rectum
Developmental stage
Eighth decade stage
Disease
Colorectal cancer
Sex
Male
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
•
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
Natural killer cell
+9
Natural killer cell
Nose skin
Nose skin
77-year-old stage
77-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Basal cell
Schwann cell
Endothelial cell of vascular tree
Basal cell of epidermis
Cell of skeletal muscle
Pericyte
Suprabasal keratinocyte
Fibroblast
Chondrocyte
Tissue
Nose skin
Developmental stage
77-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-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
ArrayExpress BioStudies:E-MTAB-13085
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
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-12595
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010038
EGA dataset:EGAD00001010017
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12698
ArrayExpress BioStudies:E-MTAB-12421
ArrayExpress BioStudies:E-MTAB-12650
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of hepatic sinusoid
+19
Endothelial cell of hepatic sinusoid
Liver
Liver
10-month-old stage
10-month-old stage
Metabolic dysfunction-associated steatotic liver disease
Metabolic dysfunction-associated steatotic liver disease
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Endothelial cell of hepatic sinusoid
Neutrophil
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Cytotoxic t cell
Kupffer cell
Intermediate monocyte
Plasmacytoid dendritic cell
Hepatic stellate cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Innate lymphoid cell
Cholangiocyte
Mesothelial cell
B cell
Peritoneal macrophage
Basophil
Conventional dendritic cell
Fibroblast
Tissue
Liver
Developmental stage
10-month-old stage
Disease
Metabolic dysfunction-associated steatotic liver disease
Sex
Male
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
Natural killer cell
+13
Natural killer cell
Skin of cheek
Skin of cheek
85-year-old stage
85-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
Natural killer cell
Endothelial cell of lymphatic vessel
Basal cell
Smooth muscle cell
Endothelial cell of vascular tree
Basal cell of epidermis
Macrophage
Regulatory t cell
Plasma cell
Pericyte
Suprabasal keratinocyte
Conventional dendritic cell
Fibroblast
Dendritic cell
Tissue
Skin of cheek
Developmental stage
85-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
Neutrophil
+15
Neutrophil
Heart left ventricle
Heart left ventricle
Seventh decade stage
Seventh decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neutrophil
Endothelial cell of lymphatic vessel
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Glial cell
Plasma cell
Vein endothelial cell
Cd14-positive monocyte
Mesothelial cell
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
Seventh 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
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
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
Airway submucosal gland duct basal cell
+22
Airway submucosal gland duct basal 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
Airway submucosal gland duct basal cell
Ciliated cell
Endothelial cell of lymphatic vessel
Lung secretory cell
Non-myelinating schwann cell
Lung interstitial macrophage
Iga plasma cell
Blood vessel smooth muscle cell
Basal cell
Endothelial cell of artery
Igg plasma cell
Bronchus fibroblast of lung
Lung macrophage
Goblet cell
Serous secreting cell of bronchus submucosal gland
Vein endothelial cell
Respiratory tract suprabasal cell
Lung perichondrial fibroblast
Adventitial cell
Fibroblast
Pulmonary alveolar type 2 cell
Lung pericyte
Chondrocyte
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
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Intestine goblet cell
+18
Intestine goblet cell
Ileum
Ileum
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Intestine goblet cell
Intestinal crypt stem cell of large intestine
Secretory cell
Neuroendocrine cell
Interstitial cell of cajal
Leukocyte
Gut absorptive cell
Gut endothelial cell
Group 3 innate lymphoid cell
Enteric smooth muscle cell
Enterocyte
Motor neuron
Interneuron
Pericyte
Progenitor cell
Intestinal crypt stem cell of small intestine
Monocyte
Myofibroblast cell
Fibroblast
Tissue
Ileum
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
GEO series:GSE158702
GEO series:GSE158328
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endocardial cell
+10
Endocardial cell
Apex of heart
Apex of heart
Seventh decade stage
Seventh decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endocardial cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Vein endothelial cell
Pericyte
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Apex of heart
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac pacemaker cell of sinoatrial node
+28
Cardiac pacemaker cell of sinoatrial node
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
Cardiac pacemaker cell of sinoatrial node
Neutrophil
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Activated cd4-positive, alpha-beta t cell
Endothelial cell
Mast cell
Cd8-positive, alpha-beta t cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Innate lymphoid cell
Glial cell
Vein endothelial cell
Cd14-positive monocyte
Cd14-low, cd16-positive monocyte
B cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Regular atrial cardiac myocyte
Monocyte
Fibroblast of cardiac tissue
Effector memory cd8-positive, alpha-beta t cell
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-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+8
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
55-year-old stage
55-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
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
55-year-old stage
Disease
Normal
Sex
Female
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
EGA Study:EGAS00001006330
Zenodo record:6578617#.YvQwQuzMI1w
Zenodo record:6578047#.YvQwPezMI1w
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
CELLxGENE
4,992 cells
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+7
Cardiac endothelial cell
Heart left ventricle
Heart left ventricle
43-year-old stage
43-year-old stage
Myocardial infarction
Myocardial infarction
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac endothelial 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
43-year-old stage
Disease
Myocardial infarction
Sex
Female
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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