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893
Nucleus
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of artery
+5
Endothelial cell of artery
Interventricular septum
Interventricular septum
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
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Vein endothelial cell
Tissue
Interventricular septum
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-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
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
Plasmacytoid dendritic cell
+29
Plasmacytoid dendritic cell
Colon
Colon
66-year-old stage
66-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
Intestine goblet cell
Natural killer cell
Dendritic cell
Transit amplifying cell of small intestine
Erythroid lineage cell
Motor neuron
Leukocyte
Intestinal crypt stem cell of large intestine
Progenitor cell
B cell
Glial cell
Neural cell
Enterocyte
Gut endothelial cell
Pericyte
Secretory cell
Intestinal crypt stem cell of small intestine
Neuroendocrine cell
Myofibroblast cell
Enteroendocrine cell
Macrophage
Group 3 innate lymphoid cell
Naive t cell
Inhibitory motor neuron
Interstitial cell of cajal
Transit amplifying cell of colon
Enteric smooth muscle cell
Gut absorptive cell
Fibroblast
Tissue
Colon
Developmental stage
66-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158702
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
+8
Cardiac muscle myoblast
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
Cardiac muscle myoblast
Neuronal receptor cell
Pericyte
Cardiac endothelial cell
Lymphoid lineage restricted progenitor 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
Myocardial infarction
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
EGA Study:EGAS00001006330
Zenodo record:6578617#.YvQwQuzMI1w
Zenodo record:6578047#.YvQwPezMI1w
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
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
Natural killer cell
+20
Natural killer cell
Right colon
Right colon
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Goblet cell
Regulatory t cell
B cell
Enterocyte
Pericyte
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Malignant cell
Smooth muscle cell
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Macrophage
Cd8-positive, alpha-beta t cell
T follicular helper cell
Igg plasma cell
Inflammatory macrophage
Stromal cell
Transit amplifying cell of colon
Enteroglial cell
Mast cell
Tissue
Right colon
Developmental stage
Eighth decade stage
Disease
Colorectal cancer
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:7760264
Zenodo record:7744244
Github:alberto-valdeolivas/ST_CRC_CMS
CELLxGENE
4,992 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+4
Hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
Prime adult stage
Primary sclerosing cholangitis
Primary sclerosing cholangitis
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Centrilobular region hepatocyte
Intrahepatic cholangiocyte
Periportal region hepatocyte
Blood cell
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Disease
Primary sclerosing cholangitis
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
nature.com
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE240429
CELLxGENE
4,992 cells
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+18
Schwann cell
Hindlimb
Hindlimb
Carnegie stage 23
Carnegie stage 23
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Reticulocyte
Osteoblast
Endothelial cell of artery
Pericyte
Muscle cell
Smooth muscle cell
Mesenchymal cell
Macrophage
Basal cell
Fibroblast of dermis
Megakaryocyte
Tendon cell
Hypertrophic chondrocyte
Chondrocyte
Articular chondrocyte
Vein endothelial cell
Fibroblast
Peridermal cell
Tissue
Hindlimb
Developmental stage
Carnegie stage 23
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Human Cell Atlas Developmental:embryonic-limb
ArrayExpress BioStudies:E-MTAB-10514
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-10367
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
+22
Goblet cell
Bronchus
Bronchus
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
Goblet cell
Bronchus fibroblast of lung
Alveolar macrophage
Respiratory tract suprabasal cell
Adventitial cell
Ciliated cell
Memory b cell
Lung macrophage
Iga plasma cell
Non-myelinating schwann cell
Lung perichondrial fibroblast
Muscle cell
Myofibroblast cell
Lung secretory cell
Basal cell
Erythrocyte
Blood vessel smooth muscle cell
Igg plasma cell
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Plasmablast
Vein endothelial cell
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ENA Project:PRJEB52292
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
+8
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
52-year-old stage
52-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 muscle myoblast
Neuronal receptor cell
Pericyte
Cardiac endothelial cell
Lymphoid lineage restricted progenitor cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Mast cell
Tissue
Heart left ventricle
Developmental stage
52-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
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Cd14-low, cd16-positive monocyte
+24
Cd14-low, cd16-positive monocyte
Sinoatrial node
Sinoatrial node
Third decade stage
Third 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
Regular atrial cardiac myocyte
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
Dendritic cell, human
Endocardial cell
Vein endothelial cell
Plasma cell
Mast cell
Mucosal invariant t cell
Cardiac pacemaker cell of sinoatrial node
Tissue
Sinoatrial node
Developmental stage
Third 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
Pulmonary alveolar type 2 cell
+20
Pulmonary alveolar type 2 cell
Bronchus
Bronchus
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
Pulmonary alveolar type 2 cell
Myoepithelial cell
Goblet cell
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Lung perichondrial fibroblast
Muscle cell
Fibroblast of lung
Myofibroblast cell
Lung secretory cell
Basal cell
Blood vessel smooth muscle cell
Cd14-positive monocyte
Blood vessel endothelial cell
Serous secreting cell of bronchus submucosal gland
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Sanger Dataset:5locationslung
ENA Project:PRJEB52292
Bioimage Archive:S-BIAD570
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
+19
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
Dendritic cell
Transit amplifying cell of small intestine
Leukocyte
Intestinal crypt stem cell of large intestine
Progenitor cell
Enterocyte
Gut endothelial cell
Pericyte
Secretory cell
Intestinal crypt stem cell of small intestine
Neuroendocrine cell
Myofibroblast cell
Macrophage
Inhibitory motor neuron
Interstitial cell of cajal
Transit amplifying cell of colon
Enteric smooth muscle cell
Interneuron
Fibroblast
Tissue
Ileum
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158702
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
Schwann cell
+6
Schwann cell
Thymus
Thymus
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
Schwann cell
T cell
Pericyte
Smooth muscle cell
Endothelial cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
16th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Bioimage Archive:S-BIAD1257
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