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896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
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2346
datasets
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
+11
Natural killer cell
Nose skin
Nose skin
91-year-old stage
91-year-old stage
Basal cell carcinoma
Basal cell carcinoma
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
Endothelial cell of vascular tree
Basal cell of epidermis
Regulatory t cell
Plasma cell
Pericyte
Suprabasal keratinocyte
Fibroblast
Dendritic cell
Tissue
Nose skin
Developmental stage
91-year-old stage
Disease
Basal cell carcinoma
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
spatial-skin-atlas.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-13085
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Mast cell
+10
Mast cell
Heart left ventricle
Heart left ventricle
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
Mast cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Adipocyte
Macrophage
Vein endothelial cell
Mesothelial cell
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
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-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12916
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
+23
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
Non-myelinating schwann cell
Mast 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
Lung macrophage
Fibroblast of lung
Vein endothelial cell
Cd14-positive monocyte
Lung perichondrial fibroblast
Naive thymus-derived cd4-positive, alpha-beta t cell
Pulmonary artery endothelial cell
Adventitial cell
Myofibroblast cell
Fibroblast
Pulmonary alveolar type 2 cell
Lung pericyte
Tissue
Bronchus
Developmental stage
Eighth decade stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
ENA Project:PRJEB52292
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
ArrayExpress BioStudies:E-MTAB-11640
Sanger Dataset:5locationslung
Bioimage Archive:S-BIAD570
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
+22
Muscle cell
Hindlimb
Hindlimb
Carnegie stage 23
Carnegie stage 23
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Muscle cell
Endothelial cell of lymphatic vessel
Erythrocyte
Fibroblast of dermis
Peridermal cell
Hypertrophic chondrocyte
Tendon cell
Basal cell
Endothelial cell of artery
Schwann cell
Smooth muscle cell
Articular chondrocyte
Connective tissue cell
Macrophage
Vein endothelial cell
Mesenchymal cell
Megakaryocyte
Pericyte
Neuron
Reticulocyte
Fibroblast
Chondrocyte
Muscle fibroblast
Tissue
Hindlimb
Developmental stage
Carnegie stage 23
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
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-8813
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
+3
Periportal region hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
Prime adult stage
Primary sclerosing cholangitis
Primary sclerosing cholangitis
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Periportal region hepatocyte
Hepatocyte
Centrilobular region hepatocyte
Intrahepatic cholangiocyte
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Disease
Primary sclerosing cholangitis
Sex
Female
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
•
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
Endothelial cell of lymphatic vessel
+9
Endothelial cell of lymphatic vessel
Skin of breast
Skin of breast
42-year-old stage
42-year-old stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Basal cell
Schwann cell
Smooth muscle cell
Endothelial cell of vascular tree
Basal cell of epidermis
Macrophage
Pericyte
Suprabasal keratinocyte
Fibroblast
Tissue
Skin of breast
Developmental stage
42-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-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
ArrayExpress BioStudies:E-MTAB-13085
CELLxGENE
4,992 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Cycling b cell
+10
Cycling b cell
Spleen
Spleen
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
Cycling b cell
Erythroid lineage cell
Epithelial cell
Megakaryocyte progenitor cell
Macrophage
Mature b cell
Megakaryocyte
Mesothelial cell
Vascular associated smooth muscle cell
Myofibroblast cell
Fibroblast
Tissue
Spleen
Developmental stage
16th 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
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
ArrayExpress BioStudies:E-MTAB-11343
BroadInstitute Single-Cell Portal:SCP1843
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
Iga plasma cell
Inflammatory macrophage
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
•
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
Endothelial cell of vascular tree
+6
Endothelial cell of vascular tree
Nose skin
Nose skin
77-year-old stage
77-year-old stage
Normal
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Endothelial cell of vascular tree
Basal cell of epidermis
Cell of skeletal muscle
Pericyte
Suprabasal keratinocyte
Fibroblast
Chondrocyte
Tissue
Nose skin
Developmental stage
77-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
ArrayExpress BioStudies:E-MTAB-13084
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
CELLxGENE
4,992 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Mature nk t cell
+8
Mature nk t cell
Interventricular septum
Interventricular septum
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
Mature nk t cell
Endothelial cell of artery
Smooth muscle cell of the pulmonary artery
Macrophage
Glial cell
Vein endothelial cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Interventricular septum
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-12916
ArrayExpress BioStudies:E-MTAB-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
CELLxGENE
4,992 cells
•
Li et al., 2022
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Epithelial cell of proximal tubule segment 1
+7
Epithelial cell of proximal tubule segment 1
Kidney
Kidney
Sixth decade stage
Sixth decade stage
Nonpapillary renal cell carcinoma
Nonpapillary renal cell carcinoma
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney pelvis urothelial cell
Kidney loop of henle thick ascending limb epithelial cell
Epithelial cell of proximal tubule segment 3
Naive thymus-derived cd4-positive, alpha-beta t cell
Collagen secreting cell
Fibroblast
Tissue
Kidney
Developmental stage
Sixth decade stage
Disease
Nonpapillary renal cell carcinoma
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
DOI:10.17632/g67bkbnhhg.1
EGA dataset:EGAD00001008030
Github:ThomasJamesMitchell/deSCeRNAMut
Sanger Institute Project:microenvironment-of-kidney-cancer
Github:ruoyan-li/RCC-spatial-mapping
EGA dataset:EGAD00001008781
HumanCellAtlas:8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1
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
+6
T cell
Thymus
Thymus
19th week post-fertilization stage
19th week post-fertilization stage
Normal
Normal
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Smooth muscle cell
Epithelial cell
Pericyte
Granulocyte monocyte progenitor cell
Fibroblast
Dendritic cell
Tissue
Thymus
Developmental stage
19th 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:GSE271304
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
GEO series:GSE206710
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