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Tissue
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Disease
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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
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Adipocyte of breast
+7
Adipocyte of breast
Breast
Breast
Prime adult stage
Prime adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Adipocyte of breast
Endothelial cell of lymphatic vessel
Mammary gland epithelial cell
Luminal epithelial cell of mammary gland
Endothelial cell of vascular tree
B cell
Pericyte
Fibroblast
Tissue
Breast
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
GEO series:GSE195665
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
Osteoblast
+18
Osteoblast
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
Osteoblast
Muscle cell
Fibroblast of dermis
Peridermal cell
Hypertrophic chondrocyte
Tendon cell
Basal cell
Endothelial cell of artery
Schwann cell
Smooth muscle cell
Articular chondrocyte
Macrophage
Vein endothelial cell
Mesenchymal cell
Megakaryocyte
Pericyte
Reticulocyte
Fibroblast
Chondrocyte
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
•
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
+5
Endothelial cell
Labial gland
Labial gland
61-year-old stage
+1
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
Endothelial cell
Iga plasma cell
Duct epithelial cell
Acinar cell of salivary gland
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
61-year-old stage
67-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
•
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
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 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
52-year-old stage
Disease
Myocardial infarction
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
EGA Study:EGAS00001006330
Zenodo record:6578617#.YvQwQuzMI1w
Zenodo record:6578553#.YvQwPezMI1w
Zenodo record:6578047#.YvQwPezMI1w
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
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
Periportal region hepatocyte
+4
Periportal region 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
Periportal region hepatocyte
Hepatocyte
Centrilobular region hepatocyte
Blood cell
Intrahepatic cholangiocyte
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell, human
+11
Dendritic cell, human
Atrioventricular node
Atrioventricular 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
Dendritic cell, human
Endothelial cell of lymphatic vessel
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Glial cell
Regular atrial cardiac myocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Atrioventricular 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
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endocardial cell
+9
Endocardial cell
Right cardiac atrium
Right cardiac atrium
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
Endocardial cell
Dendritic cell, human
T-helper 2 cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Macrophage
Glial cell
Regular atrial cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Right cardiac atrium
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
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
4,992 cells
•
Coutant et al., 2023
Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes
Explore
h5ad
Homo sapiens
Homo sapiens
Perivascular cell
+5
Perivascular cell
Breast
Breast
Adult stage
Adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
B cell
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE213688
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
+16
Cardiac pacemaker cell of sinoatrial node
Atrioventricular node
Atrioventricular node
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
Cardiac pacemaker cell of sinoatrial node
Neutrophil
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Vein endothelial cell
Cd14-low, cd16-positive monocyte
Pericyte
Regular atrial cardiac myocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Atrioventricular node
Developmental stage
Eighth 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
•
Coutant et al., 2023
Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes
Explore
h5ad
Homo sapiens
Homo sapiens
Perivascular cell
+5
Perivascular cell
Breast
Breast
Adult stage
Adult stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Perivascular cell
Endothelial cell
Epithelial cell
Myeloid cell
B cell
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE213688
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
+5
T 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
T cell
Endothelial cell
Schwann cell
Epithelial cell
Pericyte
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
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
•
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
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
Endothelial cell
Epithelial cell
Macrophage
B cell
Pericyte
Fibroblast
Tissue
Thymus
Developmental stage
17th week post-fertilization stage
Disease
Normal
Sex
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
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