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Technology
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Cell
896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
6,780 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
+13
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
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal 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
6,777 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+7
T cell
Adipose tissue
Adipose tissue
20-month-old stage and over
+1
20-month-old stage and over
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Endothelial cell
Epithelial cell
Lymphocyte
Myeloid cell
Mesenchymal stem cell of adipose tissue
B cell
Erythroblast
Tissue
Adipose tissue
Developmental stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
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
Bgee
6,751 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Ornithorhynchus anatinus (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Ornithorhynchus anatinus (h5ad)
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Early spermatid
+4
Early spermatid
Testis
Testis
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Male
Male
10x genomics v3
10x genomics v3
Organism
Ornithorhynchus anatinus
Cell type
Early spermatid
Late spermatid
Obsolete somatic cell
Spermatocyte
Spermatogonium
Tissue
Testis
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v3
Suspension type
Related Links
ebi.ac.uk
CELLxGENE
6,744 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
+13
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
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal 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
6,709 cells
•
Apostolov et al., 2024
Profiling of epithelial functional states and fibroblast phenotypes in hormone therapy-naïve localised prostate cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Smooth muscle cell of prostate
+2
Smooth muscle cell of prostate
Prostate gland
Prostate gland
69-year-old stage
+14
69-year-old stage
Prostatic acinar adenocarcinoma
Prostatic acinar adenocarcinoma
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Smooth muscle cell of prostate
Pericyte
Vascular associated smooth muscle cell
Tissue
Prostate gland
Developmental stage
69-year-old stage
75-year-old stage
71-year-old stage
61-year-old stage
54-year-old stage
68-year-old stage
72-year-old stage
59-year-old stage
64-year-old stage
45-year-old stage
62-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
63-year-old stage
Disease
Prostatic acinar adenocarcinoma
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE145843
CELLxGENE
6,674 cells
•
Choksi et al., 2024
An alternative cell cycle coordinates multiciliated cell differentiation
Explore
h5ad
Mus musculus
Mus musculus
Tracheal epithelial cell
Tracheal epithelial cell
Tracheal epithelial cell
Tracheal epithelial cell
Mature stage
Mature stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Tracheal epithelial cell
Tissue
Tracheal epithelial cell
Developmental stage
Mature stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE228110
Github:lb15/multiciliation_cycle
Zenodo record:10896066
Zenodo record:10896071
Zenodo record:10896100
CELLxGENE
6,671 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of hepatic sinusoid
+19
Endothelial cell of hepatic sinusoid
Liver
Liver
10-month-old stage
10-month-old stage
Normal
+1
Normal
Male
Male
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Mus musculus
Cell type
Endothelial cell of hepatic sinusoid
Neutrophil
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Cytotoxic t cell
Kupffer cell
Intermediate monocyte
Plasmacytoid dendritic cell
Hepatic stellate cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Innate lymphoid cell
Cholangiocyte
Mesothelial cell
B cell
Peritoneal macrophage
Basophil
Conventional dendritic cell
Fibroblast
Tissue
Liver
Developmental stage
10-month-old stage
Disease
Normal
Metabolic dysfunction-associated steatotic liver disease
Sex
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
CELLxGENE
6,639 cells
•
Serizay et al., 2025
Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis
Explore
h5ad
Mus musculus
Mus musculus
Multiciliated ependymal cell
+3
Multiciliated ependymal cell
Multiciliated ependymal cell
Multiciliated ependymal cell
Theiler stage 27
Theiler stage 27
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Multiciliated ependymal cell
Deuterosomal cell
Radial glial cell
Neuron associated cell
Tissue
Multiciliated ependymal cell
Developmental stage
Theiler stage 27
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
DOI:10.1016/j.celrep.2024.115117
GEO series:GSE201773
DOI:10.5281/zenodo.14105247
CELLxGENE
6,562 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
+13
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
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
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
6,560 cells
•
Opasawatchai et al., 2022
Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+12
T cell
Dental pulp
Dental pulp
21-year-old stage
+3
21-year-old stage
Pulpitis
+2
Pulpitis
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Endothelial cell
Schwann cell
Macrophage
Hematopoietic stem cell
Glial cell
Plasma cell
Odontoblast
B cell
Fibroblast
Dendritic cell
Non-classical monocyte
Tissue
Dental pulp
Developmental stage
21-year-old stage
26-year-old stage
36-year-old stage
20-year-old stage
Disease
Pulpitis
Enamel caries
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE185222
Github:vclabsysbio/scRNAseq_Dentalpulp
CELLxGENE
6,541 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Fast muscle cell
+17
Fast muscle cell
Tongue muscle
+2
Tongue muscle
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Microcebus murinus
Cell type
Fast muscle cell
T cell
Stromal cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Tendon cell
Endothelial cell of artery
Capillary endothelial cell
Macrophage
Vein endothelial cell
Pericyte
Skeletal muscle satellite stem cell
Vascular associated smooth muscle cell
Basophil
Fibroblast
Myelinating schwann cell
Oral mucosa squamous cell
Dendritic cell
Tissue
Tongue muscle
Tongue
Epithelium of tongue
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
UCSC Cell Browser:tabula-microcebus
app.globus.org
CELLxGENE
6,528 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Stromal cell
+8
Stromal cell
Testis
Testis
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Male
Male
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Microcebus murinus
Cell type
Stromal cell
Capillary endothelial cell
Lymphocyte
Macrophage
Spermatid
Eosinophil
Mesothelial cell
Spermatocyte
Spermatogonium
Tissue
Testis
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Male
Technology
Smart-seq2
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
app.globus.org
UCSC Cell Browser:tabula-microcebus
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