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893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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Most cells
Fewest cells
2339
datasets
CELLxGENE
3,509 cells
•
Anderson-Crannage et al., 2023
Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin
Explore
h5ad
Mus musculus
Mus musculus
Fibroblast
Fibroblast
Autopod skin
Autopod skin
2-week-old stage
2-week-old stage
Epidermolysis bullosa
+1
Epidermolysis bullosa
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Fibroblast
Tissue
Autopod skin
Developmental stage
2-week-old stage
Disease
Epidermolysis bullosa
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE222250
CELLxGENE
3,460 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:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
CELLxGENE
3,460 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
B cell
+7
B cell
Thymus
Thymus
14th week post-fertilization stage
+13
14th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
B cell
Naive b cell
Memory b cell
Large pre-b-ii cell
Pro-b cell
Small pre-b-ii cell
Late pro-b cell
Plasma cell
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
Suspension type
Cell
Related Links
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
CELLxGENE
3,457 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+8
Plasmacytoid dendritic cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
Asteria scrna-seq kit
Asteria scrna-seq kit
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Cd14-low, cd16-positive monocyte
Natural killer cell
Dendritic cell
B cell
Cd4-positive, alpha-beta t cell
Megakaryocyte
Cd14-positive monocyte
Cytotoxic t cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
Asteria scrna-seq kit
Suspension type
Cell
Related Links
Github:danledinh/scRNAseq-repo
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
CELLxGENE
3,434 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
B cell
+5
B cell
Respiratory airway
Respiratory airway
66-year-old stage
66-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
B cell
Neutrophil
Mature nk t cell
Erythrocyte
Epithelial cell
Myeloid cell
Tissue
Respiratory airway
Developmental stage
66-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
3,406 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
+8
Natural killer cell
Gonadal fat pad
Gonadal 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
Cd8-positive, alpha-beta t cell
Endothelial cell
Epithelial cell
Mesenchymal stem cell of adipose tissue
Myeloid cell
Tissue
Gonadal 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
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
3,384 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Pancreatic d cell
+8
Pancreatic d cell
Pancreas
Pancreas
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
Pancreatic d cell
Leukocyte
Pancreatic acinar cell
Type b pancreatic cell
Pancreatic stellate cell
Endothelial cell
Pancreatic pp cell
Pancreatic ductal cell
Pancreatic a cell
Tissue
Pancreas
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
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
GEO series:GSE132042
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
3,374 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:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
CELLxGENE
3,351 cells
•
Moorman et al., 2025
Author Correction: Progressive plasticity during colorectal cancer metastasis
Explore
h5ad
Homo sapiens
Homo sapiens
Malignant cell
Malignant cell
Lung
+2
Lung
45-year-old stage
45-year-old stage
Colorectal cancer
Colorectal cancer
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Malignant cell
Tissue
Lung
Liver
Rectum
Developmental stage
45-year-old stage
Disease
Colorectal cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:dpeerlab/progressive-plasticity-crc-metastasis.git
CELLxGENE
3,342 cells
•
Qiu et al., 2024
A single-cell time-lapse of mouse prenatal development from gastrula to birth
Explore
h5ad
Mus musculus
Mus musculus
Leydig cell
+1
Leydig cell
Embryo
Embryo
Theiler stage 21
+9
Theiler stage 21
Normal
Normal
Female
+1
Female
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Leydig cell
Type i cell of adrenal cortex
Tissue
Embryo
Developmental stage
Theiler stage 21
Theiler stage 27
Theiler stage 20
Theiler stage 26
Theiler stage 23
Theiler stage 19
Theiler stage 22
Theiler stage 24
Theiler stage 18
Theiler stage 25
Disease
Normal
Sex
Female
Male
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE186069
GEO series:GSE228590
Ontogeny of Mouse, Graphed
CELLxGENE
3,332 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
3,324 cells
•
Pan et al., 2024
Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profiling: a case study
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
Oligodendrocyte precursor cell
White matter of parietal lobe
+4
White matter of parietal lobe
68-year-old stage
+7
68-year-old stage
Alzheimer disease
+2
Alzheimer disease
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Tissue
White matter of parietal lobe
Prefrontal cortex
White matter of frontal lobe
White matter of occipital lobe
White matter of temporal lobe
Developmental stage
68-year-old stage
82-year-old stage
83-year-old stage
76-year-old stage
72-year-old stage
81-year-old stage
53-year-old stage
70-year-old stage
Disease
Alzheimer disease
Leukoencephalopathy, diffuse hereditary, with spheroids 1
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE267301
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