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Cell Type
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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
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Most cells
Fewest cells
2339
datasets
CELLxGENE
1,336 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
1,324 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
+6
B cell
Respiratory airway
Respiratory airway
74-year-old stage
74-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
Epithelial cell
Plasma cell
Mast cell
Myeloid cell
Tissue
Respiratory airway
Developmental stage
74-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
COVID-19 cell atlas
Github:simslab/cluster_diffex2018
CELLxGENE
1,324 cells
•
Rodríguez-Ubreva et al., 2022
Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses
Explore
h5ad
Homo sapiens
Homo sapiens
Naive b cell
+2
Naive b cell
Blood
Blood
26-year-old stage
26-year-old stage
Common variable immunodeficiency
+1
Common variable immunodeficiency
Male
Male
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Homo sapiens
Cell type
Naive b cell
Class switched memory b cell
Unswitched memory b cell
Tissue
Blood
Developmental stage
26-year-old stage
Disease
Common variable immunodeficiency
Normal
Sex
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
ENA Project:PRJEB50820
EGA dataset:EGAD00001008575
ventolab.org
carrerasresearch.org
immunodeficiencycellatlas.org
Github:ventolab/CVID
CELLxGENE
1,320 cells
•
Scala et al., 2020
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Explore
h5ad
Mus musculus
Mus musculus
Gabaergic neuron
+1
Gabaergic neuron
Primary motor cortex
Primary motor cortex
11-week-old stage
+23
11-week-old stage
Normal
Normal
Female
+1
Female
Patch-seq
Patch-seq
Cell
Cell
Organism
Mus musculus
Cell type
Gabaergic neuron
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
11-week-old stage
24-week-old stage
19-week-old stage
21-week-old stage
8-week-old stage
29-week-old stage
14-week-old stage
10-week-old stage
16-week-old stage
25-week-old stage
17-week-old stage
12-week-old stage
8-month-old stage
20-week-old stage
6-week-old stage
9-week-old stage
18-week-old stage
7-week-old stage
15-week-old stage
22-week-old stage
13-week-old stage
26-week-old stage
5-week-old stage
23-week-old stage
Disease
Normal
Sex
Female
Male
Technology
Patch-seq
Suspension type
Cell
Related Links
Andreas Tolias lab
NeMo archive:dat-kq04hua
CELLxGENE
1,295 cells
•
Joseph et al., 2020
Urethral luminal epithelia are castration‐insensitive cells of the proximal prostate
Explore
h5ad
Homo sapiens
Homo sapiens
Smooth muscle cell of prostate
+1
Smooth muscle cell of prostate
Peripheral zone of prostate
+1
Peripheral zone of prostate
31-year-old stage
+4
31-year-old stage
Benign prostatic hyperplasia
+1
Benign prostatic hyperplasia
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Smooth muscle cell of prostate
Fibroblast of connective tissue of prostate
Tissue
Peripheral zone of prostate
Transition zone of prostate
Developmental stage
31-year-old stage
57-year-old stage
74-year-old stage
72-year-old stage
29-year-old stage
Disease
Benign prostatic hyperplasia
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
strandlab.net
GEO series:GSE145928
GEO series:GSE145929
DOI:10.25548/16-WM8C
CELLxGENE
1,284 cells
•
Alkaslasi et al., 2021
Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord
Explore
h5ad
Mus musculus
Mus musculus
Motor neuron
Motor neuron
Thoracic spinal cord
+2
Thoracic spinal cord
8-week-old stage
8-week-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Motor neuron
Tissue
Thoracic spinal cord
Cervical spinal cord
Lumbar spinal cord
Developmental stage
8-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
CELLxGENE
1,281 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
Mus musculus
Mus musculus
Schwann cell
+2
Schwann cell
Cranial neural crest
Cranial neural crest
Theiler stage 21
+5
Theiler stage 21
Normal
Normal
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Schwann cell
Melanocyte
Neural crest cell
Tissue
Cranial neural crest
Developmental stage
Theiler stage 21
Theiler stage 20
Theiler stage 23
Theiler stage 19
Theiler stage 22
Theiler stage 17
Disease
Normal
Sex
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14343226
DOI:10.25550/8D-2JQ0
DOI:10.25550/7N-54BY
Github:cotneylab/craniofacial_snrna
CELLxGENE
1,250 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
B cell
+2
B cell
Caudate lobe of liver
Caudate lobe of liver
Young adult stage
+2
Young adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
B cell
Naive b cell
Plasmablast
Tissue
Caudate lobe of liver
Developmental stage
Young adult stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE115469
CELLxGENE
1,248 cells
•
Isola et al., 2024
A single-cell atlas of the aging mouse ovary
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of lymphatic vessel
+3
Endothelial cell of lymphatic vessel
Ovary
Ovary
9-month-old stage
+1
9-month-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell of lymphatic vessel
Endothelial cell of vascular tree
Epithelial cell
Granulosa cell
Tissue
Ovary
Developmental stage
9-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE232309
omrf.shinyapps.io
Github:StoutLab/OvarianAgingAtlas
Single Cell Portal
1,226 cells
Explore
Mus musculus
Mus musculus
Neuron
Neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Bgee
1,205 cells
•
Scialdone et al., 2016
Resolving early mesoderm diversification through single-cell expression profiling
Explore
scRNA-Seq full-length processed expression values per cell population in Mus musculus (tsv.gz)
scRNA-Seq full-length H5AD data per cell in Mus musculus (h5ad)
Mus musculus
Mus musculus
Epiblast cell
+1
Epiblast cell
Embryo
Embryo
Theiler stage 11c
+3
Theiler stage 11c
Normal
Normal
Smart-seq2
Smart-seq2
Organism
Mus musculus
Cell type
Epiblast cell
Mesodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 11c
Theiler stage 10
Neurula stage
Theiler stage 09
Disease
Normal
Sex
Technology
Smart-seq2
Suspension type
Related Links
ncbi.nlm.nih.gov
CELLxGENE
1,203 cells
•
Moorman et al., 2025
Author Correction: Progressive plasticity during colorectal cancer metastasis
Explore
h5ad
Homo sapiens
Homo sapiens
Malignant cell
Malignant cell
Liver
+1
Liver
55-year-old stage
55-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
Liver
Sigmoid colon
Developmental stage
55-year-old stage
Disease
Colorectal cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:dpeerlab/progressive-plasticity-crc-metastasis.git
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