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Cell
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
•
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
B cell
+4
B cell
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
Prime adult stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
B cell
Centrilobular region hepatocyte
Endothelial cell
Periportal region hepatocyte
Blood cell
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
nature.com
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE240429
GEO series:GSE247128
GEO series:GSE245620
CELLxGENE
4,992 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+3
Hepatocyte
Liver
Liver
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
Hepatocyte
Cholangiocyte
Endothelial cell of periportal hepatic sinusoid
Macrophage
Tissue
Liver
Developmental stage
59-year-old stage
Disease
Normal
Sex
Female
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
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+17
Regular atrial cardiac myocyte
Right cardiac atrium
Right cardiac atrium
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
Regular atrial cardiac myocyte
T-helper 2 cell
Endothelial cell of artery
Glial cell
Neutrophil
Mature nk t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Endothelial cell
Cd14-positive monocyte
Dendritic cell, human
Endocardial cell
Vein endothelial cell
Mast cell
Mesothelial cell
Tissue
Right cardiac atrium
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
ArrayExpress BioStudies:E-MTAB-12916
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
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
+4
T cell
Thymus
Thymus
13th week post-fertilization stage
13th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Pericyte
Smooth muscle cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
13th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Bioimage Archive:S-BIAD1257
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
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
+6
Dendritic cell
Thymus
Thymus
2-year-old stage
2-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
T cell
B cell
Smooth muscle cell
Macrophage
Endothelial cell
Epithelial cell
Tissue
Thymus
Developmental stage
2-year-old stage
Disease
Normal
Sex
Male
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
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Enterocyte
+9
Enterocyte
Colon
Colon
Prime adult stage
Prime adult stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Enterocyte
Endothelial cell of lymphatic vessel
Neutrophil
Monocyte
Transit amplifying cell
Myofibroblast cell
Stem cell
Enteric neuron
Germinal center b cell
Fibroblast
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Sanger Dataset:treg-gut-niches
ENA Project:PRJEB57700
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+9
Regular atrial cardiac myocyte
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
Regular atrial cardiac myocyte
T-helper 2 cell
Endothelial cell of artery
Glial cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Smooth muscle cell of the pulmonary artery
Dendritic cell, human
Endocardial cell
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-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
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
+6
Cardiac muscle myoblast
Heart left ventricle
Heart left ventricle
51-year-old stage
51-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
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
51-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
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578617#.YvQwQuzMI1w
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
+15
Plasmacytoid dendritic cell
Liver
Liver
Young adult stage
Young adult stage
Normal
Normal
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
Neutrophil
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Intermediate monocyte
Erythrocyte
Endothelial cell of pericentral hepatic sinusoid
Vascular associated smooth muscle cell
Hematopoietic stem cell
Fibroblast
Tissue
Liver
Developmental stage
Young adult stage
Disease
Normal
Sex
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
•
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
Schwann cell
+16
Schwann cell
Lung
Lung
19th week post-fertilization stage
19th week post-fertilization stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Schwann cell
Pulmonary alveolar type 2 cell
Club cell
Lung multiciliated epithelial cell
Epithelial cell of lung
Neuron
Endothelial cell of lymphatic vessel
Fibroblast of lung
Myofibroblast cell
Tracheobronchial smooth muscle cell
Lung secretory cell
Basal cell
Respiratory tract epithelial cell
Vascular associated smooth muscle cell
Chondrocyte
Pulmonary alveolar type 1 cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
19th 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
•
Pranzatelli et al., 2024
GZMK+CD8+ T cells Target A Specific Acinar Cell Type in Sjögren’s Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+5
Dendritic cell
Labial gland
Labial gland
40-year-old stage
40-year-old stage
Immune system disorder
+1
Immune system disorder
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
Iga plasma cell
Duct epithelial cell
Igg plasma cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
40-year-old stage
Disease
Immune system disorder
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
+21
Pulmonary alveolar type 2 cell
Lung parenchyma
Lung parenchyma
Seventh decade stage
Seventh decade 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
Naive thymus-derived cd4-positive, alpha-beta t cell
Alveolar macrophage
Club cell
Endothelial cell of artery
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Muscle cell
Fibroblast of lung
Erythrocyte
Blood vessel smooth muscle cell
Megakaryocyte
Igg plasma cell
Blood vessel endothelial cell
Pulmonary artery endothelial cell
Pulmonary alveolar type 1 cell
Plasmablast
Vein endothelial cell
Tissue
Lung parenchyma
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Male
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
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