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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
3,406 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+8
T cell
Gonadal fat pad
Gonadal fat pad
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Natural killer cell
Endothelial cell
Cd8-positive, alpha-beta t cell
Epithelial cell
Myeloid cell
Cd4-positive, alpha-beta t cell
Mesenchymal stem cell of adipose tissue
B cell
Tissue
Gonadal fat pad
Developmental stage
3-month-old stage
20-month-old stage and over
18-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
3,384 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+8
Endothelial cell
Pancreas
Pancreas
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell
Pancreatic acinar cell
Pancreatic pp cell
Leukocyte
Pancreatic a cell
Pancreatic d cell
Pancreatic stellate cell
Type b pancreatic cell
Pancreatic ductal cell
Tissue
Pancreas
Developmental stage
3-month-old stage
20-month-old stage and over
18-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
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
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm 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
3,351 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
Type i cell of adrenal cortex
+1
Type i cell of adrenal cortex
Embryo
Embryo
Theiler stage 22
+9
Theiler stage 22
Normal
Normal
Female
+1
Female
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Type i cell of adrenal cortex
Leydig cell
Tissue
Embryo
Developmental stage
Theiler stage 22
Theiler stage 27
Theiler stage 24
Theiler stage 18
Theiler stage 25
Theiler stage 19
Theiler stage 26
Theiler stage 20
Theiler stage 21
Theiler stage 23
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
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm 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
3,324 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
Prefrontal cortex
+4
Prefrontal cortex
53-year-old stage
+7
53-year-old stage
Normal
+2
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Tissue
Prefrontal cortex
White matter of temporal lobe
White matter of frontal lobe
White matter of occipital lobe
White matter of parietal lobe
Developmental stage
53-year-old stage
68-year-old stage
82-year-old stage
72-year-old stage
81-year-old stage
70-year-old stage
76-year-old stage
83-year-old stage
Disease
Normal
Alzheimer disease
Leukoencephalopathy, diffuse hereditary, with spheroids 1
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE267301
CELLxGENE
3,316 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm 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
3,294 cells
•
Khouri-Farah et al., 2025
Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+2
Schwann cell
Cranial neural crest
Cranial neural crest
Carnegie stage 14
+5
Carnegie stage 14
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Schwann cell
Melanocyte
Neural crest cell
Tissue
Cranial neural crest
Developmental stage
Carnegie stage 14
Carnegie stage 13
Carnegie stage 20
Carnegie stage 17
Carnegie stage 12
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14343226
DOI:10.25550/8D-2JQ0
DOI:10.25550/7N-54BY
Github:cotneylab/craniofacial_snrna
Single Cell Portal
3,290 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+6
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Microglial cell
Brain microvascular endothelial cell
Obsolete excitatory neuron
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD718) (section 250)
Corresponding registered brain section (MD718) (section 251)
Corresponding registered brain section (MD718) (section 252)
CELLxGENE
3,282 cells
•
Nowicki-Osuch et al., 2023
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Explore
h5ad
Homo sapiens
Homo sapiens
Mast cell
+3
Mast cell
Duodenum
+8
Duodenum
69-year-old stage
+25
69-year-old stage
Barrett esophagus
+3
Barrett esophagus
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Mast cell
Macrophage
Monocyte
Dendritic cell
Tissue
Duodenum
Ileum
Colon
Submucosal esophageal gland
Body of stomach
Cardia of stomach
Rectum
Esophagogastric junction
Lower esophagus
Developmental stage
69-year-old stage
34-year-old stage
42-year-old stage
43-year-old stage
53-year-old stage
54-year-old stage
68-year-old stage
48-year-old stage
29-year-old stage
56-year-old stage
55-year-old stage
50-year-old stage
51-year-old stage
57-year-old stage
74-year-old stage
80 year-old and over stage
58-year-old stage
67-year-old stage
77-year-old stage
45-year-old stage
62-year-old stage
41-year-old stage
60-year-old stage
63-year-old stage
83-year-old stage
27-year-old stage
Disease
Barrett esophagus
Normal
Gastric intestinal metaplasia
Gastritis
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001010074
Github:karolno/BE-GIM_Comparison
CELLxGENE
3,282 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Stromal cell
+3
Stromal cell
Mammary gland
Mammary gland
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Stromal cell
Endothelial cell
Basal cell
Luminal epithelial cell of mammary gland
Tissue
Mammary gland
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
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
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