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Tissue
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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
3,589 cells
•
Darmanis et al., 2017
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
+6
Oligodendrocyte precursor cell
Cerebral cortex
Cerebral cortex
54-year-old stage
+3
54-year-old stage
Glioblastoma
Glioblastoma
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular lymphangioblast
Myeloid cell
Neoplastic cell
Neuron
Astrocyte
Tissue
Cerebral cortex
Developmental stage
54-year-old stage
48-year-old stage
55-year-old stage
60-year-old stage
Disease
Glioblastoma
Sex
Technology
Smart-seq2
Suspension type
Cell
Related Links
UCSC Cell Browser:quake-gbm
HumanCellAtlas:2d846095-8a33-4f3c-97d4-585bafac13b4
GEO series:GSE84465
gbmseq.org
Single Cell Expression Atlas Experiment:E-GEOD-84465
Single Cell Portal
3,583 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+3
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Obsolete excitatory neuron
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD704) (section 107)
CELLxGENE
3,553 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
Single Cell Portal
3,541 cells
Explore
Mus musculus
Mus musculus
Neuron
Neuron
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
3,536 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Cardiac muscle cell
Cardiac muscle cell
Heart
Heart
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Cardiac muscle cell
Tissue
Heart
Developmental stage
Pharyngula:prim-15
Hatching:long-pec
Larval:protruding-mouth
Pharyngula:prim-25
Segmentation:26+ somites
Segmentation:14-19 somites
Hatching:pec-fin
Segmentation:20-25 somites
Pharyngula:high-pec
Pharyngula:prim-5
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
CELLxGENE
3,526 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Gabaergic neuron
Gabaergic neuron
Hippocampal formation
Hippocampal formation
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Gabaergic neuron
Tissue
Hippocampal formation
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:dat-1je0mn3
submit.brainimagelibrary.org
CELLxGENE
3,524 cells
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmablast
Plasmablast
Breast
Breast
42-year-old stage
+10
42-year-old stage
Invasive ductal breast carcinoma
+1
Invasive ductal breast carcinoma
Female
Female
10x 5' v1
+2
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmablast
Tissue
Breast
Developmental stage
42-year-old stage
52-year-old stage
54-year-old stage
55-year-old stage
82-year-old stage
57-year-old stage
49-year-old stage
67-year-old stage
60-year-old stage
63-year-old stage
47-year-old stage
Disease
Invasive ductal breast carcinoma
Invasive lobular breast carcinoma
Sex
Female
Technology
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
EGA Study:EGAS00001005173
Zenodo record:4739739
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
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
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Small pre-b-ii cell
+7
Small pre-b-ii cell
Thymus
Thymus
13th week post-fertilization stage
+13
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Small pre-b-ii cell
Pro-b cell
Late pro-b cell
Memory b cell
Large pre-b-ii cell
Plasma cell
B cell
Naive b cell
Tissue
Thymus
Developmental stage
13th week post-fertilization stage
2-year-old stage
3-month-old stage
14th week post-fertilization stage
15th week post-fertilization stage
17th week post-fertilization stage
12th week post-fertilization stage
6-month-old stage
18th week post-fertilization stage
10-month-old stage
2-month-old stage
Newborn stage (0-28 days)
5-month-old stage
14-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
EGA dataset:EGAD00001015384
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
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:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
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
Natural killer cell
+8
Natural killer 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
Natural killer cell
Cytotoxic t cell
Plasmacytoid dendritic cell
Cd4-positive, alpha-beta t cell
Cd14-positive monocyte
Megakaryocyte
Cd14-low, cd16-positive monocyte
B cell
Dendritic 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
Neutrophil
+5
Neutrophil
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
Neutrophil
Erythrocyte
Mature nk t cell
Epithelial cell
Myeloid cell
B 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
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