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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
•
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
Extravillous trophoblast
Uterine smooth muscle cell
Epithelial cell
Placental villous trophoblast
Embryonic fibroblast
Syncytiotrophoblast 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:EGAD00001010017
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12698
ArrayExpress BioStudies:E-MTAB-12421
EGA dataset:EGAD00001010038
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
Endothelial tip cell
+20
Endothelial tip cell
Rectum
Rectum
Sixth decade stage
Sixth decade stage
Colorectal cancer
Colorectal cancer
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial tip cell
Stromal cell
Endothelial cell of lymphatic vessel
Mast cell
Cd8-positive, alpha-beta t cell
Iga plasma cell
Smooth muscle cell
Enteroglial cell
Igg plasma cell
Goblet cell
Transit amplifying cell of colon
Macrophage
Regulatory t cell
Endothelial stalk cell
Enterocyte
Cd4-positive, alpha-beta t cell
Malignant cell
B cell
Pericyte
Myofibroblast cell
Conventional dendritic cell
Tissue
Rectum
Developmental stage
Sixth decade stage
Disease
Colorectal cancer
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Zenodo record:7744244
Github:alberto-valdeolivas/ST_CRC_CMS
Zenodo record:7760264
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
12th week post-fertilization stage
12th 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
Erythrocyte
Pulmonary neuroendocrine cell
Basal cell
Endothelial cell of artery
Respiratory tract epithelial cell
Bronchus fibroblast of lung
Pulmonary alveolar type 1 cell
Fibroblast of lung
Vein endothelial cell
Megakaryocyte
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
12th 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-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
•
Kuppe et al., 2022
Spatial multi-omic map of human myocardial infarction
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac endothelial cell
+6
Cardiac endothelial cell
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 endothelial cell
Mast cell
Lymphoid lineage restricted progenitor cell
Immature innate lymphoid cell
Cardiac muscle myoblast
Smooth muscle myoblast
Fibroblast of cardiac tissue
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
Github:KramannLab/visium_heart
Zenodo record:6580069#.YvQwROzMI1w
kramannlab.com
Zenodo record:6578047#.YvQwPezMI1w
EGA Study:EGAS00001006330
HumanCellAtlas:e9f36305-d857-44a3-93f0-df4e6007dc97
Zenodo record:6578553#.YvQwPezMI1w
Github:saezlab/visium_heart
Zenodo record:6578617#.YvQwQuzMI1w
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
+11
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
Decidual natural killer cell, human
Endothelial cell of uterus
Placental villous trophoblast
Endothelial cell of placenta
Embryonic fibroblast
Syncytiotrophoblast 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
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12698
ArrayExpress BioStudies:E-MTAB-12421
EGA dataset:EGAD00001010017
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
+10
Endothelial cell
Labial gland
Labial gland
48-year-old stage
+1
48-year-old stage
Sjogren syndrome
+1
Sjogren syndrome
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell
Iga plasma cell
Ionocyte
Smooth muscle cell
Myoepithelial cell
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Duct epithelial cell
Acinar cell of salivary gland
Fibroblast
Dendritic cell
Tissue
Labial gland
Developmental stage
48-year-old stage
56-year-old stage
Disease
Sjogren syndrome
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
Muscle cell
+30
Muscle 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
Muscle cell
Airway submucosal gland duct basal cell
Blood vessel endothelial cell
Ciliated cell
Endothelial cell of lymphatic vessel
Lung secretory cell
Non-myelinating schwann cell
Lung interstitial macrophage
Iga plasma cell
Blood vessel smooth muscle cell
Basal cell
Endothelial cell of artery
Smooth muscle cell of the pulmonary artery
Igg plasma cell
Bronchus fibroblast of lung
Myoepithelial cell
Lung macrophage
Memory b cell
Pulmonary alveolar type 1 cell
Serous secreting cell of bronchus submucosal gland
Fibroblast of lung
Vein endothelial cell
Cd14-positive monocyte
Respiratory tract suprabasal cell
Lung perichondrial fibroblast
Adventitial cell
Naive b cell
Fibroblast
Pulmonary alveolar type 2 cell
Lung pericyte
Chondrocyte
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
•
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
+5
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
B 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:GSE115469
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE240429
GEO series:GSE243977
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endocardial cell
+18
Endocardial cell
Heart right ventricle
Heart right ventricle
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
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Cd8-positive, alpha-beta t cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Plasma cell
Vein endothelial cell
Mesothelial cell
Pericyte
Mucosal invariant t cell
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart right ventricle
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-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
CELLxGENE
4,992 cells
Explore
h5ad
Mus musculus
Mus musculus
Double-positive, alpha-beta thymocyte
+3
Double-positive, alpha-beta thymocyte
Thymus
Thymus
6-week-old stage
6-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
Cd4-positive, alpha-beta thymocyte
Epithelial cell of thymus
Tissue
Thymus
Developmental stage
6-week-old stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
CELLxGENE
4,992 cells
•
Gu et al., 2024
Immune microniches shape intestinal Treg function
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+9
Neutrophil
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
Neutrophil
Germinal center b cell
Endothelial cell of lymphatic vessel
Enteric neuron
Stem cell
Enterocyte
Transit amplifying cell
Monocyte
Myofibroblast 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
CELLxGENE
4,992 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+10
T cell
Thymus
Thymus
18th week post-fertilization stage
18th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Cycling t cell
Alpha-beta t cell
Medullary thymic epithelial cell type 3
Medullary thymic epithelial cell type 1
Double-positive, alpha-beta thymocyte
Epithelial cell
Cd4-positive, alpha-beta thymocyte
Conventional dendritic cell
Fibroblast
Dendritic cell
Tissue
Thymus
Developmental stage
18th week post-fertilization stage
Disease
Normal
Sex
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Human Cell Atlas Developmental:fetal-immune
Teichmann lab
UCSC Cell Browser:fetal-immune
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
BroadInstitute Single-Cell Portal:SCP1843
ArrayExpress BioStudies:E-MTAB-11341
ArrayExpress BioStudies:E-MTAB-11343
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
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