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Tissue
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Disease
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Technology
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Cell
896
Nucleus
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
•
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
+18
Tracheobronchial smooth muscle 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
Tracheobronchial smooth muscle cell
Club cell
Erythrocyte
Pulmonary neuroendocrine cell
Endothelial cell of artery
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Bronchus fibroblast of lung
Macrophage
Pulmonary alveolar type 1 cell
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Vein endothelial cell
Mesothelial cell
Pulmonary interstitial fibroblast
Epithelial cell of lung
Vascular associated smooth muscle cell
Myofibroblast cell
Pulmonary alveolar type 2 cell
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-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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+2
T 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
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
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
ENA Project:PRJEB77091
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of artery
+8
Endothelial cell of artery
Apex of heart
Apex of heart
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
Endothelial cell of artery
Smooth muscle cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Vein endothelial cell
Pericyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Apex of heart
Developmental stage
Seventh decade stage
Disease
Normal
Sex
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
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
T cell
+3
T 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
T cell
Epithelial cell
Myeloid cell
Malignant 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
Endocardial cell
+14
Endocardial cell
Left cardiac atrium
Left 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
Endocardial cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Vein endothelial cell
Cd14-low, cd16-positive monocyte
Mesothelial cell
Pericyte
Regular atrial cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Left 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-12916
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
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
+9
Endothelial cell
Labial gland
Labial gland
52-year-old stage
+1
52-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Smooth muscle cell
Duct epithelial cell
Acinar cell of salivary gland
Cd4-positive, alpha-beta t cell
B cell
Cd8-positive, alpha-beta regulatory t cell
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
52-year-old stage
54-year-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:pranzatelli/scRNAseqNM2023
dbGaP Study:phs002446
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
Stromal cell
+13
Stromal cell
Right colon
Right colon
Eighth decade stage
Eighth decade stage
Colorectal cancer
Colorectal cancer
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Stromal cell
Endothelial cell of lymphatic vessel
Iga plasma cell
Smooth muscle cell
Igg plasma cell
Goblet cell
Transit amplifying cell of colon
Macrophage
Endothelial stalk cell
Enterocyte
Malignant cell
B cell
Pericyte
Myofibroblast cell
Tissue
Right colon
Developmental stage
Eighth decade stage
Disease
Colorectal cancer
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:7760264
Zenodo record:7744244
Github:alberto-valdeolivas/ST_CRC_CMS
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Double-positive, alpha-beta thymocyte
+4
Double-positive, alpha-beta thymocyte
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
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
•
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
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
Tracheobronchial smooth muscle cell
Club cell
Erythrocyte
Endothelial cell of artery
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Bronchus fibroblast of lung
Large pre-b-ii cell
Pulmonary alveolar type 1 cell
Fibroblast of lung
Cd4-positive, alpha-beta t cell
Pulmonary interstitial fibroblast
Pericyte
Epithelial cell of lung
Vascular associated smooth muscle cell
Pulmonary alveolar type 2 cell
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-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
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Muscle cell
+11
Muscle cell
Hindlimb
Hindlimb
Carnegie stage 19
Carnegie stage 19
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Muscle cell
Fibroblast of dermis
Tendon cell
Basal cell
Schwann cell
Primitive red blood cell
Chondroblast
Vein endothelial cell
Mesenchymal cell
Megakaryocyte
Fibroblast
Chondrocyte
Tissue
Hindlimb
Developmental stage
Carnegie stage 19
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
•
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
Periportal region hepatocyte
+4
Periportal region hepatocyte
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
Periportal region hepatocyte
Hepatocyte
Centrilobular region hepatocyte
Endothelial cell
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:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
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
6-month-old stage
6-month-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Epithelial cell
Macrophage
Myelocyte
B cell
Tissue
Thymus
Developmental stage
6-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
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