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Technology
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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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Most cells
Fewest cells
2339
datasets
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
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 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
55-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
Github:KramannLab/visium_heart
EGA Study:EGAS00001006330
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
Pericyte
+8
Pericyte
Sigmoid colon
Sigmoid colon
Seventh decade stage
Seventh decade stage
Colorectal cancer
Colorectal cancer
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Pericyte
Malignant cell
Smooth muscle cell
Myofibroblast cell
Macrophage
Endothelial tip cell
Inflammatory macrophage
Endothelial cell
Endothelial stalk cell
Tissue
Sigmoid colon
Developmental stage
Seventh decade stage
Disease
Colorectal cancer
Sex
Female
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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+3
Dendritic cell
Thymus
Thymus
18th week post-fertilization stage
18th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
T cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
18th week post-fertilization 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
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
ccgg.ugent.be
Github:Teichlab/TissueTag
GEO series:GSE206710
CELLxGENE
4,992 cells
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary alveolar type 2 cell
+22
Pulmonary alveolar type 2 cell
Lung
Lung
20th week post-fertilization stage
20th week post-fertilization 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
Bronchus fibroblast of lung
Club cell
Lung multiciliated epithelial cell
Epithelial cell of lung
Pericyte
Endothelial cell of lymphatic vessel
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Tracheobronchial smooth muscle cell
Cd8-positive, alpha-beta t cell
Basal cell
Respiratory tract epithelial cell
Erythrocyte
Group 3 innate lymphoid cell
Megakaryocyte
Vascular associated smooth muscle cell
Capillary endothelial cell
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary neuroendocrine cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
20th week post-fertilization stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11267
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
Natural killer cell
+18
Natural killer 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
Natural killer cell
Myoepithelial cell
Dendritic cell
T cell
Naive b cell
Memory b cell
Endothelial cell of lymphatic vessel
Monocyte
Malignant cell
Mature nk t cell
Perivascular cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Luminal epithelial cell of mammary gland
Endothelial cell
Plasmablast
Fibroblast
Myeloid 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
EGA Study:EGAS00001005173
Zenodo record:4739739
CELLxGENE
4,992 cells
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary alveolar type 2 cell
+18
Pulmonary alveolar type 2 cell
Lung
Lung
12th week post-fertilization stage
12th week post-fertilization 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
Bronchus fibroblast of lung
Club cell
Endothelial cell of artery
Epithelial cell of lung
Neuron
Fibroblast of lung
Myofibroblast cell
Tracheobronchial smooth muscle cell
Basal cell
Respiratory tract epithelial cell
Erythrocyte
Megakaryocyte
Vascular associated smooth muscle cell
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary neuroendocrine cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
12th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
ArrayExpress BioStudies:E-MTAB-11278
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
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
Pubis
Pubis
52-year-old stage
52-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
Dendritic cell
Regulatory t cell
Pericyte
Endothelial cell of lymphatic vessel
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Plasma cell
Tissue
Pubis
Developmental stage
52-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
•
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
Dendritic cell
Regulatory t cell
Basal cell of epidermis
Pericyte
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Smooth muscle cell
Macrophage
Basal cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Fibroblast
Plasma 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
•
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
B cell
+4
B cell
Breast
Breast
Adult stage
Adult stage
Triple-negative breast carcinoma
Triple-negative breast carcinoma
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
B cell
Malignant cell
Epithelial cell
Fibroblast
Myeloid cell
Tissue
Breast
Developmental stage
Adult stage
Disease
Triple-negative breast carcinoma
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
Naive thymus-derived cd4-positive, alpha-beta t cell
+25
Naive thymus-derived cd4-positive, alpha-beta t cell
Atrioventricular node
Atrioventricular node
Sixth decade stage
Sixth decade stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Naive thymus-derived cd4-positive, alpha-beta t cell
Regular atrial cardiac myocyte
Atrioventricular bundle cell
Endothelial cell of artery
Regular ventricular cardiac myocyte
Glial cell
Pericyte
Endothelial cell of lymphatic vessel
Neutrophil
Monocyte
Cd8-positive, alpha-beta cytotoxic t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Endothelial cell
Dendritic cell, human
Capillary endothelial cell
Endocardial cell
Vein endothelial cell
Plasma cell
Mast cell
Mucosal invariant t cell
Cardiac pacemaker cell of sinoatrial node
Cd16-positive, cd56-dim natural killer cell, human
Tissue
Atrioventricular node
Developmental stage
Sixth 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
+7
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
64-year-old stage
64-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
Adipocyte of epicardial fat of left ventricle
Cardiac endothelial cell
Lymphoid lineage restricted progenitor cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Tissue
Heart left ventricle
Developmental stage
64-year-old stage
Disease
Myocardial infarction
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:6578553#.YvQwPezMI1w
Zenodo record:6580069#.YvQwROzMI1w
Github:saezlab/visium_heart
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
Github:KramannLab/visium_heart
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
CELLxGENE
4,992 cells
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Extravillous trophoblast
+6
Extravillous trophoblast
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
Extravillous trophoblast
Endothelial cell of lymphatic vessel
Stromal cell
Trophoblast giant cell
Endothelial cell of uterus
Uterine smooth muscle cell
Epithelial 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
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