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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
+4
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
61-year-old stage
61-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Cardiac muscle myoblast
Cardiac endothelial cell
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
Tissue
Heart left ventricle
Developmental stage
61-year-old stage
Disease
Normal
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
Zenodo record:6578047#.YvQwPezMI1w
Zenodo record:6578617#.YvQwQuzMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
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
+17
Plasmacytoid dendritic cell
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
Plasmacytoid dendritic cell
Hepatocyte
Hepatic stellate cell
Endothelial cell of hepatic sinusoid
Peritoneal macrophage
Cholangiocyte
B cell
Conventional dendritic cell
Neutrophil
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Macrophage
Intermediate monocyte
Erythrocyte
Endothelial cell of pericentral hepatic sinusoid
Basophil
Fibroblast
Mesothelial cell
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
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+12
Schwann cell
Hindlimb
Hindlimb
Carnegie stage 16
Carnegie stage 16
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Osteoblast
Endothelial cell of artery
Skeletal muscle myoblast
Muscle cell
Smooth muscle cell
Mesenchymal cell
Chondroblast
Primitive red blood cell
Basal cell
Fibroblast of dermis
Tendon cell
Chondrocyte
Tissue
Hindlimb
Developmental stage
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Human Cell Atlas Developmental:embryonic-limb
ArrayExpress BioStudies:E-MTAB-10367
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-10514
CELLxGENE
4,992 cells
•
Glasner et al., 2023
Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies
Explore
h5ad
Mus musculus
Mus musculus
Alveolar macrophage
+7
Alveolar macrophage
Lung
Lung
5-month-old stage
5-month-old stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Alveolar macrophage
B cell
Ciliated cell
Pericyte
Macrophage
Pulmonary alveolar type 1 cell
Epithelial cell
Fibroblast
Tissue
Lung
Developmental stage
5-month-old stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
humantumoratlas.org
Github:dpeerlab/Treg_depletion_reproducibility
dbGaP Study:phs002371
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
+22
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
Connective tissue cell
Endothelial cell of artery
Neuron
Pericyte
Endothelial cell of lymphatic vessel
Muscle cell
Smooth muscle cell
Mesenchymal cell
Muscle fibroblast
Macrophage
Basal cell
Fibroblast of dermis
Erythrocyte
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-10367
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
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
+24
Pulmonary alveolar type 2 cell
Lung
Lung
16th week post-fertilization stage
16th 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
Dendritic cell
Bronchus fibroblast of lung
Bone marrow cell
Club cell
Lung multiciliated epithelial cell
Epithelial cell of lung
Neuron
Endothelial cell of lymphatic vessel
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Macrophage
Tracheobronchial smooth muscle cell
Cd8-positive, alpha-beta t cell
Respiratory tract epithelial cell
Erythrocyte
Vascular associated smooth muscle cell
Capillary endothelial cell
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary neuroendocrine cell
Pulmonary interstitial fibroblast
Mesothelial cell
Tissue
Lung
Developmental stage
16th week post-fertilization stage
Disease
Normal
Sex
Male
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
•
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
Bronchus fibroblast of lung
+16
Bronchus fibroblast of lung
Lung
Lung
14th week post-fertilization stage
14th week post-fertilization stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Bronchus fibroblast of lung
Club cell
Endothelial cell of artery
Epithelial cell of lung
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Tracheobronchial smooth muscle cell
Cd8-positive, alpha-beta t cell
Respiratory tract epithelial cell
Erythrocyte
Megakaryocyte
Vascular associated smooth muscle cell
Capillary endothelial cell
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
14th 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-11267
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
CELLxGENE
4,992 cells
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Decidual natural killer cell, human
+11
Decidual natural killer cell, human
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
Decidual natural killer cell, human
Extravillous trophoblast
Endothelial cell of lymphatic vessel
Syncytiotrophoblast cell
Stromal cell
Trophoblast giant cell
Placental villous trophoblast
Endothelial cell of placenta
Embryonic fibroblast
Hofbauer cell
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
CELLxGENE
4,992 cells
•
Glasner et al., 2023
Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies
Explore
h5ad
Mus musculus
Mus musculus
Alveolar macrophage
+11
Alveolar macrophage
Lung
Lung
5-month-old stage
5-month-old stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Alveolar macrophage
B cell
Ciliated cell
Cell of skeletal muscle
Pericyte
Myofibroblast cell
Macrophage
Capillary endothelial cell
Pulmonary alveolar type 1 cell
Epithelial cell
Fibroblast
Mesothelial cell
Tissue
Lung
Developmental stage
5-month-old stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
humantumoratlas.org
Github:dpeerlab/Treg_depletion_reproducibility
dbGaP Study:phs002371
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
+9
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
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
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
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
•
Li et al., 2022
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Naive thymus-derived cd4-positive, alpha-beta t cell
+16
Naive thymus-derived cd4-positive, alpha-beta t cell
Kidney
Kidney
Seventh decade stage
Seventh decade stage
Nonpapillary renal cell carcinoma
Nonpapillary renal cell carcinoma
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
Podocyte
Pericyte
Iga plasma cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Cd4-positive, alpha-beta t cell
Epithelial cell of proximal tubule
Macrophage
Cd8-positive, alpha-beta t cell
Igg plasma cell
Kidney loop of henle ascending limb epithelial cell
Endothelial cell
Epithelial cell of proximal tubule segment 1
Collagen secreting cell
Fibroblast
Mast cell
Tissue
Kidney
Developmental stage
Seventh decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
DOI:10.17632/g67bkbnhhg.1
EGA dataset:EGAD00001008030
EGA dataset:EGAD00001008781
Github:ThomasJamesMitchell/deSCeRNAMut
Sanger Institute Project:microenvironment-of-kidney-cancer
Github:ruoyan-li/RCC-spatial-mapping
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
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
+10
Schwann cell
Skin of forehead
Skin of forehead
55-year-old stage
55-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
Regulatory t cell
Basal cell of epidermis
Cell of skeletal muscle
Pericyte
Smooth muscle cell
Endothelial cell of vascular tree
Suprabasal keratinocyte
Chondrocyte
Fibroblast
Tissue
Skin of forehead
Developmental stage
55-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
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
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