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Cell Type
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Tissue
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Disease
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Sex
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Technology
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Cell
896
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
Single Cell Portal
1,486 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
Astrocyte of the cerebellum
Obsolete excitatory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD704) (section 107)
CELLxGENE
1,465 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Caudal ganglionic eminence derived interneuron
Caudal ganglionic eminence derived interneuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Caudal ganglionic eminence derived interneuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
knowledge.brain-map.org
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
Allen Brain Map:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
CELLxGENE
1,417 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
Hepatic stellate cell
+2
Hepatic stellate cell
Caudate lobe of liver
Caudate lobe of liver
Late adult stage
+2
Late adult stage
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Hepatic stellate cell
Vein endothelial cell
Vascular associated smooth muscle cell
Tissue
Caudate lobe of liver
Developmental stage
Late adult stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
nature.com
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE240429
CELLxGENE
1,387 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
Pancreatic endocrine cell
+3
Pancreatic endocrine cell
Endocrine pancreas
Endocrine pancreas
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Pancreatic endocrine cell
Pancreatic a cell
Pancreatic d cell
Type b pancreatic cell
Tissue
Endocrine pancreas
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
1,378 cells
•
Orozco et al., 2020
Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
S cone cell
+1
S cone cell
Retina
Retina
65-year-old stage
+3
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
S cone cell
Retinal cone cell
Tissue
Retina
Developmental stage
65-year-old stage
77-year-old stage
70-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE135133
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
CELLxGENE
1,374 cells
•
Andrews et al., 2021
Single‐Cell, Single‐Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Hepatic stellate cell
+2
Hepatic stellate cell
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Hepatic stellate cell
Vascular associated smooth muscle cell
Fibroblast
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Nucleus
Related Links
Github:tallulandrews/Liver_sc_sn_paper_scripts
HumanCellAtlas:8a666b76-daaf-4b1f-9414-e4807a1d1e8b
macparlandlab.shinyapps.io
GEO series:GSE185477
protocols.io:human-liver-caudate-lobe-dissociation-for-scrna-se-q26g77j1gwz1/v2
ASAP
1,349 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Hemocyte
+5
Hemocyte
Fat body
Fat body
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Organism
Drosophila melanogaster
Cell type
Hemocyte
Epithelial cell
Muscle cell
Adult neuron
Sensory neuron
Adult oenocyte
Tissue
Fat body
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
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
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
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
Unswitched memory b cell
+2
Unswitched memory b cell
Blood
Blood
26-year-old stage
26-year-old stage
Normal
+1
Normal
Male
Male
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Homo sapiens
Cell type
Unswitched memory b cell
Naive b cell
Class switched memory b cell
Tissue
Blood
Developmental stage
26-year-old stage
Disease
Normal
Common variable immunodeficiency
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
1,324 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
Neutrophil
+6
Neutrophil
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
Neutrophil
Mature nk t cell
Mast cell
Epithelial cell
Myeloid cell
Plasma cell
B 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
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
1,320 cells
•
Scala et al., 2020
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
+1
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
22-week-old stage
+23
22-week-old stage
Normal
Normal
Female
+1
Female
Patch-seq
Patch-seq
Cell
Cell
Organism
Mus musculus
Cell type
Glutamatergic neuron
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
22-week-old stage
5-week-old stage
9-week-old stage
15-week-old stage
13-week-old stage
24-week-old stage
21-week-old stage
26-week-old stage
12-week-old stage
20-week-old stage
14-week-old stage
29-week-old stage
19-week-old stage
18-week-old stage
25-week-old stage
11-week-old stage
7-week-old stage
6-week-old stage
8-month-old stage
10-week-old stage
23-week-old stage
17-week-old stage
16-week-old stage
8-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
Fibroblast of connective tissue of prostate
+1
Fibroblast of connective tissue of prostate
Transition zone of prostate
+1
Transition zone of prostate
29-year-old stage
+4
29-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
Fibroblast of connective tissue of prostate
Smooth muscle cell of prostate
Tissue
Transition zone of prostate
Peripheral zone of prostate
Developmental stage
29-year-old stage
57-year-old stage
72-year-old stage
74-year-old stage
31-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
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