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Cell Type
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Tissue
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Disease
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Technology
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Cell
893
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
3,076 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
3,055 cells
•
The Tabula Sapiens Consortium* et al., 2022
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
Explore
h5ad
Homo sapiens
Homo sapiens
Melanocyte
+15
Melanocyte
Crista ampullaris
+1
Crista ampullaris
60-year-old stage
+1
60-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Melanocyte
B cell
Pericyte
Neutrophil
Monocyte
Cd4-positive, alpha-beta t cell
Macrophage
Intermediate monocyte
Cd8-positive, alpha-beta t cell
Endothelial cell of vascular tree
Supporting cell of vestibular epithelium
Vascular associated smooth muscle cell
Stromal cell
Hematopoietic cell
Mast cell
Vestibular dark cell
Tissue
Crista ampullaris
Utricle of membranous labyrinth
Developmental stage
60-year-old stage
45-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
AWS Open Data:tabula-sapiens
CZ BioHub Portal:tabula-sapiens-portal
HumanCellAtlas:10201832-7c73-4033-9b65-3ef13d81656a
UCSC Cell Browser:tabula-sapiens
DOI:10.1101/2024.12.03.626516
UCSC Genome Browser:hgTrackUi?hgsid=1437536541_FfasmBrAlAiA7oFphu1csVv0KHgc&db=hg38&c=chrX&g=tabulaSapiens
CELLxGENE
3,052 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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
3,045 cells
•
Fink et al., 2022
Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of artery
+3
Endothelial cell of artery
Ureter
Ureter
68-year-old stage
+8
68-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of artery
Smooth muscle cell
Vein endothelial cell
Fibroblast
Tissue
Ureter
Developmental stage
68-year-old stage
82-year-old stage
75-year-old stage
74-year-old stage
81-year-old stage
79-year-old stage
65-year-old stage
85-year-old stage
69-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE184111
GEO series:GSE184112
UCSC Cell Browser:adult-ureter
Zenodo record:6762182
Github:2019surbhi/tinglab_ureter_analysis
CELLxGENE
3,014 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Natural killer cell
+9
Natural killer cell
Mesenteric fat pad
Mesenteric fat pad
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Natural killer cell
T cell
B cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Endothelial cell
Epithelial cell
Mesenchymal stem cell of adipose tissue
Myeloid cell
Tissue
Mesenteric fat pad
Developmental stage
20-month-old stage and over
18-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
GEO series:GSE132042
CZ BioHub Portal:tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CELLxGENE
2,988 cells
•
Vinsland et al., 2025
Organotypic Timelapse recording with Transcriptomic Readout (OTTR) links cell behaviour to cell identity in human tissues
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+4
Astrocyte
Telencephalon
Telencephalon
10th week post-fertilization stage
10th week post-fertilization stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Astrocyte
Forebrain neuroblast
Glioblast
Gabaergic neuron
Glutamatergic neuron
Tissue
Telencephalon
Developmental stage
10th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/OTTR
Single Cell Portal
2,986 cells
Explore
Mus musculus musculus
Mus musculus musculus
Plasmacytoid dendritic cell
+12
Plasmacytoid dendritic cell
Normal
Normal
10x 3' v1
10x 3' v1
Organism
Mus musculus musculus
Cell type
Plasmacytoid dendritic cell
Goblet cell
Tuft cell
T cell
Erythroid progenitor cell
B cell
Enterocyte
Paneth cell
Enteroendocrine cell
Cell
Epithelial cell
Fibroblast
Professional antigen presenting cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v1
Suspension type
CELLxGENE
2,958 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatocyte
+8
Hepatocyte
Liver
Liver
55-year-old stage
55-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Hepatocyte
T cell
B cell
Monocyte
Malignant cell
Mature nk t cell
Macrophage
Endothelial cell
Fibroblast
Tissue
Liver
Developmental stage
55-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
2,951 cells
•
Chan et al., 2021
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+3
Plasmacytoid dendritic cell
Lung
+5
Lung
62-year-old stage
+13
62-year-old stage
Small cell lung carcinoma
Small cell lung carcinoma
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Conventional dendritic cell
Neutrophil
Classical monocyte
Tissue
Lung
Adrenal gland
Pleural effusion
Liver
Lymph node
Axilla
Developmental stage
62-year-old stage
64-year-old stage
68-year-old stage
55-year-old stage
75-year-old stage
77-year-old stage
74-year-old stage
72-year-old stage
67-year-old stage
47-year-old stage
81-year-old stage
69-year-old stage
70-year-old stage
71-year-old stage
Disease
Small cell lung carcinoma
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
Single Cell Portal
2,947 cells
Explore
Mus musculus
Mus musculus
Oligodendrocyte
+4
Oligodendrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Oligodendrocyte
Astrocyte
Obsolete excitatory neuron
Oligodendrocyte precursor cell
Obsolete inhibitory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD704) (section 425)
CELLxGENE
2,923 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+2
Plasmacytoid dendritic cell
Thymus
Thymus
14th week post-fertilization stage
+13
14th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+3
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Conventional dendritic cell
Macrophage
Tissue
Thymus
Developmental stage
14th week post-fertilization stage
10-month-old stage
14-month-old stage
5-month-old stage
2-month-old stage
15th week post-fertilization stage
6-month-old stage
2-year-old stage
13th week post-fertilization stage
12th week post-fertilization stage
18th week post-fertilization stage
17th week post-fertilization stage
3-month-old stage
Newborn stage (0-28 days)
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v2
10x 5' v1
10x 3' v3
Suspension type
Cell
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
Single Cell Portal
2,901 cells
Explore
Mus musculus
Mus musculus
Oligodendrocyte
+6
Oligodendrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Oligodendrocyte
Obsolete excitatory neuron
Microglial cell
Oligodendrocyte precursor cell
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Astrocyte of the cerebellum
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD703) (section 584)
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184
185
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