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Technology
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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
5,039 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of artery
+18
Endothelial cell of artery
Heart right ventricle
Heart right ventricle
Seventh decade stage
+1
Seventh decade stage
Normal
Normal
Female
+1
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
Pericyte
Endothelial cell of lymphatic vessel
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
Dendritic cell, human
Endocardial cell
Vein endothelial cell
Plasma cell
Mucosal invariant t cell
Mesothelial cell
Cd16-positive, cd56-dim natural killer cell, human
Tissue
Heart right ventricle
Developmental stage
Seventh decade stage
Sixth decade stage
Disease
Normal
Sex
Female
Male
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
5,038 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Notochordal cell
+15
Notochordal cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Notochordal cell
Spinal cord interneuron
Paraxial cell
Neurectodermal cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Anterior visceral endoderm cell
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
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
+11
Hepatocyte
Liver
Liver
59-year-old stage
59-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Hepatocyte
Cholangiocyte
B cell
Non-classical monocyte
Conventional dendritic cell
Kupffer cell
Endothelial cell of periportal hepatic sinusoid
Macrophage
Erythrocyte
Vascular associated smooth muscle cell
Fibroblast
Plasma cell
Tissue
Liver
Developmental stage
59-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
livercellatlas.org
GEO series:GSE192742
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
Pulmonary alveolar type 2 cell
+14
Pulmonary alveolar type 2 cell
Lung
Lung
17th week post-fertilization stage
17th 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
Club cell
Lung multiciliated epithelial cell
Epithelial cell of lung
Fibroblast of lung
Myofibroblast cell
Tracheobronchial smooth muscle cell
Respiratory tract epithelial cell
Megakaryocyte
Vascular associated smooth muscle cell
Chondrocyte
Pulmonary alveolar type 1 cell
Vein endothelial cell
Pulmonary interstitial fibroblast
Mesothelial cell
Tissue
Lung
Developmental stage
17th 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-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11265
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
+23
Pulmonary alveolar type 2 cell
Bronchus
Bronchus
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
Pulmonary alveolar type 2 cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Endothelial cell of artery
Adventitial cell
Ciliated cell
Lung macrophage
Iga plasma cell
Non-myelinating schwann cell
Lung perichondrial fibroblast
Muscle cell
Lung pericyte
Fibroblast of lung
Myofibroblast cell
Basal cell
Blood vessel smooth muscle cell
Smooth muscle cell of the pulmonary artery
Cd14-positive monocyte
Blood vessel endothelial cell
Pulmonary artery endothelial cell
Lung interstitial macrophage
Vein endothelial cell
Fibroblast
Mast cell
Airway submucosal gland duct basal cell
Tissue
Bronchus
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Immature single positive thymocyte
+5
Immature single positive thymocyte
Thymus
Thymus
21-day-old stage
21-day-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Immature single positive thymocyte
Epithelial cell of thymus
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Endothelial cell
Cd4-positive, alpha-beta thymocyte
Double-positive, alpha-beta thymocyte
Tissue
Thymus
Developmental stage
21-day-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
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
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
Fibroblast of cardiac tissue
Immature innate lymphoid cell
Smooth muscle myoblast
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
•
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
+9
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
Myofibroblast cell
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
dbGaP Study:phs002371
Github:dpeerlab/Treg_depletion_reproducibility
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
58-year-old stage
58-year-old stage
Sjogren syndrome
Sjogren syndrome
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
Cd4-positive, alpha-beta t cell
Fibroblast
Acinar cell of salivary gland
Tissue
Labial gland
Developmental stage
58-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
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+13
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
Regulatory t cell
Mesenchymal cell
Myofibroblast cell
Macrophage
Alpha-beta t cell
Medullary thymic epithelial cell type 1
Vascular associated smooth muscle cell
Corticomedullary thymic epithelial cell
B-1 b cell
Cd4-positive, alpha-beta thymocyte
Epithelial cell
Fibroblast
Double-positive, alpha-beta thymocyte
Tissue
Thymus
Developmental stage
16th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Teichmann lab
Github:Teichlab/Pan_fetal_immune
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
BroadInstitute Single-Cell Portal:SCP1843
Human Cell Atlas Developmental:fetal-immune
UCSC Cell Browser:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
DOI:10.1016/j.stem.2018.12.011
ArrayExpress BioStudies:E-MTAB-11341
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
+15
Pulmonary alveolar type 2 cell
Lung
Lung
14th week post-fertilization stage
14th 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
Lung multiciliated epithelial cell
Epithelial cell of lung
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Myofibroblast cell
Tracheobronchial smooth muscle cell
Respiratory tract epithelial cell
Megakaryocyte
Vascular associated smooth muscle cell
Pulmonary alveolar type 1 cell
Pulmonary neuroendocrine cell
Pulmonary interstitial fibroblast
Tissue
Lung
Developmental stage
14th week post-fertilization stage
Disease
Normal
Sex
Female
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
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Enterocyte
+8
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
Neutrophil
Transit amplifying cell
Myofibroblast cell
Stem cell
Enteric neuron
Germinal center b cell
Epithelial cell
Fibroblast
Tissue
Colon
Developmental stage
Prime adult stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB57700
Sanger Dataset:treg-gut-niches
1
2
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144
145
146
147
148
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389
390
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