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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
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Most cells
Fewest cells
2346
datasets
CELLxGENE
6,190 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
Oligodendrocyte
Striatum
+22
Striatum
13th week post-fertilization stage
+10
13th week post-fertilization stage
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Oligodendrocyte
Tissue
Striatum
Medulla oblongata
Hindbrain
Cortex
Midbrain
Dorsal plus ventral thalamus
Lower layers of the cortex
Frontal cortex
Entorhinal cortex
Midbrain tectum
Metencephalon
Basal forebrain
Cerebellum
Brain
Hypothalamus
Cerebellar peduncular complex
Upper layers of the cortex
Caudate-putamen
Hippocampal formation
Pons
Cerebral subcortex
Occipital cortex
Forebrain
Developmental stage
13th week post-fertilization stage
14th week post-fertilization stage
15th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 22
Carnegie stage 16
Carnegie stage 18
11th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001006049
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
CELLxGENE
6,177 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
6,171 cells
•
Yao et al., 2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
+6
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
Smart-seq v4
Smart-seq v4
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Glutamatergic neuron
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Microglial cell
Astrocyte
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq v4
Suspension type
Nucleus
Related Links
NeMo archive:dat-ch1nqb7
DOI:10.17504/protocols.io.pjvdkn6
DOI:10.17504/protocols.io.bcbrism6
CELLxGENE
6,142 cells
•
Zhao et al., 2025
A cell and transcriptome atlas of human arterial vasculature
Explore
h5ad
Homo sapiens
Homo sapiens
Blood vessel smooth muscle cell
+5
Blood vessel smooth muscle cell
Aorta
Aorta
46-year-old stage
46-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Blood vessel smooth muscle cell
Endothelial cell of artery
Lymphocyte
Macrophage
Microcirculation associated smooth muscle cell
Fibroblast
Tissue
Aorta
Developmental stage
46-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:zhaoshuoxp/czi_rna
HumanCellAtlas:2245bca0-6563-4e88-ab26-f2b8f60383a7
CELLxGENE
6,133 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Near-projecting glutamatergic cortical neuron
Near-projecting glutamatergic cortical neuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Near-projecting glutamatergic cortical neuron
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:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
CELLxGENE
6,101 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
A2 amacrine cell
+3
A2 amacrine 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
A2 amacrine cell
Glycinergic amacrine cell
Amacrine cell
Starburst amacrine 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
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
Bgee
6,092 cells
•
Michki et al., 2021
The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis
Explore
scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster (h5ad)
Drosophila melanogaster
Drosophila melanogaster
Larval optic neuroblast
+1
Larval optic neuroblast
Insect embryonic/larval brain
Insect embryonic/larval brain
Late third instar larval stage
Late third instar larval stage
Normal
Normal
10x genomics v2
+1
10x genomics v2
Organism
Drosophila melanogaster
Cell type
Larval optic neuroblast
Type ii neuroblast
Tissue
Insect embryonic/larval brain
Developmental stage
Late third instar larval stage
Disease
Normal
Sex
Technology
10x genomics v2
10x genomics v3
Suspension type
Related Links
SRA Project:SRP269777
CELLxGENE
6,051 cells
•
Kaya et al., 2022
CD8+ T cells induce interferon-responsive oligodendrocytes and microglia in white matter aging
Explore
h5ad
Mus musculus
Mus musculus
Oligodendrocyte
Oligodendrocyte
Brain white matter
+1
Brain white matter
20-month-old stage and over
20-month-old stage and over
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Oligodendrocyte
Tissue
Brain white matter
Brain gray matter
Developmental stage
20-month-old stage and over
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
www-ncbi-nlm-nih-gov.stanford.idm.oclc.org
Github:ISD-SystemsNeuroscience/Aging_Oligos_Microglia
Single Cell Portal
6,050 cells
Explore
Homo sapiens
Homo sapiens
B cell
B cell
Covid-19
Covid-19
10x 5' v2
10x 5' v2
Organism
Homo sapiens
Cell type
B cell
Tissue
Developmental stage
Disease
Covid-19
Sex
Technology
10x 5' v2
Suspension type
CELLxGENE
6,044 cells
•
Zhang et al., 2021
Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+19
T cell
Kidney
Kidney
69-year-old stage
+4
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Podocyte
Renal principal cell
Natural killer cell
Renal beta-intercalated cell
Epithelial cell of proximal tubule
Vasa recta descending limb cell
Renal alpha-intercalated cell
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney loop of henle thick ascending limb epithelial cell
Vasa recta ascending limb cell
Mesangial cell
Kidney collecting duct cell
B cell
Pericyte
Columnar/cuboidal epithelial cell
Monocyte
Vascular associated smooth muscle cell
Glomerular capillary endothelial cell
Tissue
Kidney
Developmental stage
69-year-old stage
65-year-old stage
74-year-old stage
70-year-old stage
76-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
HumanCellAtlas:7c599029-7a3c-4b5c-8e79-e72c9a9a65fe
CELLxGENE
5,980 cells
•
Wang et al., 2019
Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
Explore
h5ad
Homo sapiens
Homo sapiens
Stem cell
+6
Stem cell
Ileum
Ileum
67-year-old stage
+1
67-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Stem cell
Transit amplifying cell of colon
Paneth cell of colon
Colon goblet cell
Progenitor cell
Colonocyte
Enteroendocrine cell of colon
Tissue
Ileum
Developmental stage
67-year-old stage
60-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
Single Cell Expression Atlas Experiment:E-GEOD-125970
GEO series:GSE125970
UCSC Cell Browser:human-intestine
Single Cell Portal
5,978 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+4
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte
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 (MD700) (section 440)
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