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896
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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
•
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
Endothelial cell
Epithelial cell
Macrophage
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
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE271304
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
Tracheobronchial smooth muscle cell
+17
Tracheobronchial smooth muscle cell
Lung
Lung
17th week post-fertilization stage
17th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Tracheobronchial smooth muscle cell
Club cell
Natural killer cell
Erythrocyte
Endothelial cell
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Bronchus fibroblast of lung
Macrophage
Pulmonary alveolar type 1 cell
Fibroblast of lung
Vein endothelial cell
Pulmonary interstitial fibroblast
Neuron
Epithelial cell of lung
Vascular associated smooth muscle cell
Pulmonary alveolar type 2 cell
Chondrocyte
Tissue
Lung
Developmental stage
17th 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
•
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
Tracheobronchial smooth muscle cell
+16
Tracheobronchial smooth muscle 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
Tracheobronchial smooth muscle cell
Club cell
Endothelial cell of lymphatic vessel
Lung secretory cell
Basal cell
Schwann cell
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Pulmonary alveolar type 1 cell
Fibroblast of lung
Pulmonary interstitial fibroblast
Neuron
Epithelial cell of lung
Vascular associated smooth muscle cell
Myofibroblast cell
Pulmonary alveolar type 2 cell
Chondrocyte
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-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
•
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
+7
Endothelial cell
Labial gland
Labial gland
56-year-old stage
+1
56-year-old stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Macrophage
Duct epithelial cell
Acinar cell of salivary gland
Cd4-positive, alpha-beta t cell
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
56-year-old stage
64-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+5
Endothelial cell
Thymus
Thymus
4-week-old stage
4-week-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Endothelial cell
Double-positive, alpha-beta thymocyte
Immature single positive thymocyte
Gamma-delta thymocyte
Cd4-positive, alpha-beta thymocyte
Epithelial cell of thymus
Tissue
Thymus
Developmental stage
4-week-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
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
+14
Natural killer cell
Skin of temple
Skin of temple
33-year-old stage
33-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Natural killer cell
Endothelial cell of lymphatic vessel
Basal cell
Schwann cell
Smooth muscle cell
Plasmacytoid dendritic cell
Endothelial cell of vascular tree
Basal cell of epidermis
Macrophage
Plasma cell
Cell of skeletal muscle
Pericyte
Suprabasal keratinocyte
Fibroblast
Chondrocyte
Tissue
Skin of temple
Developmental stage
33-year-old stage
Disease
Normal
Sex
Female
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
•
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
Epithelial cell
+4
Epithelial 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
Epithelial cell
Myeloid cell
Malignant cell
B cell
Fibroblast
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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+3
T cell
Thymus
Thymus
19-month-old stage
19-month-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Endothelial cell
Epithelial cell
B cell
Tissue
Thymus
Developmental stage
19-month-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Bioimage Archive:S-BIAD1257
CELLxGENE
4,992 cells
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Stromal cell
+6
Stromal cell
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
Stromal cell
Endothelial cell of lymphatic vessel
Trophoblast giant cell
Extravillous trophoblast
Uterine smooth muscle cell
Epithelial cell
Endothelial cell of uterus
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-12421
ArrayExpress BioStudies:E-MTAB-12595
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010038
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12698
EGA dataset:EGAD00001010017
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 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
Natural killer cell
Endothelial cell of lymphatic vessel
Cytotoxic t cell
Basal cell
Smooth muscle cell
Endothelial cell of vascular tree
Basal cell of epidermis
Regulatory t cell
Cell of skeletal muscle
Pericyte
Monocyte
Suprabasal keratinocyte
Fibroblast
Chondrocyte
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
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
ArrayExpress BioStudies:E-MTAB-13084
CELLxGENE
4,992 cells
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Transit amplifying cell of small intestine
+27
Transit amplifying cell of small intestine
Colon
Colon
66-year-old stage
66-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Transit amplifying cell of small intestine
Intestine goblet cell
Intestinal crypt stem cell of large intestine
Secretory cell
Interstitial cell of cajal
Erythroid lineage cell
Leukocyte
Gut absorptive cell
Inhibitory motor neuron
Plasmacytoid dendritic cell
Neural cell
Enteroendocrine cell
Gut endothelial cell
Group 3 innate lymphoid cell
Transit amplifying cell of colon
Macrophage
Enteric smooth muscle cell
Glial cell
Enterocyte
B cell
Pericyte
Progenitor cell
Naive t cell
Intestinal crypt stem cell of small intestine
Monocyte
Myofibroblast cell
Fibroblast
Dendritic cell
Tissue
Colon
Developmental stage
66-year-old stage
Disease
Normal
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158328
GEO series:GSE158702
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
Tracheobronchial smooth muscle cell
+15
Tracheobronchial smooth muscle 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
Tracheobronchial smooth muscle cell
Club cell
Pulmonary neuroendocrine cell
Endothelial cell of artery
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Bronchus fibroblast of lung
Pulmonary alveolar type 1 cell
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Megakaryocyte
Pulmonary interstitial fibroblast
Epithelial cell of lung
Vascular associated smooth muscle cell
Myofibroblast cell
Pulmonary alveolar type 2 cell
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-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
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