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Tissue
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Disease
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Technology
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Cell
893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
Bgee
7,727 cells
•
Kurmangaliyev et al., 2019
Modular transcriptional programs separately define axon and dendrite connectivity
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
T5d neuron
+8
T5d neuron
Embryonic/larval optic lobe
Embryonic/larval optic lobe
Pharate adult stage p8
+1
Pharate adult stage p8
Normal
Normal
Female
Female
10x genomics v2
10x genomics v2
Organism
Drosophila melanogaster
Cell type
T5d neuron
T4b neuron
T5a neuron
T5b neuron
T neuron
T4d neuron
T5c neuron
T4c neuron
T4a neuron
Tissue
Embryonic/larval optic lobe
Developmental stage
Pharate adult stage p8
Pupal stage p6
Disease
Normal
Sex
Female
Technology
10x genomics v2
Suspension type
Related Links
SRA Project:SRP184201
CELLxGENE
7,726 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
Neutrophil
+3
Neutrophil
Blood
+1
Blood
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Neutrophil
Myeloid lineage restricted progenitor cell
Macrophage
Erythrocyte
Tissue
Blood
Multicellular anatomical structure
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
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
7,689 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Choroid plexus epithelial cell
Choroid plexus epithelial cell
Superior temporal gyrus
+19
Superior temporal gyrus
42-year-old stage
+3
42-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Choroid plexus epithelial cell
Tissue
Superior temporal gyrus
Hippocampal field
Superior parietal cortex
Cerebellar nuclear complex
Pontine tegmentum
Primary motor cortex
Hypothalamus
Intralaminar nuclear group
Midbrain nucleus
Pulvinar nucleus
Midbrain tectum
Anterior nuclear group
Dentate gyrus of hippocampal formation
Pontine reticular formation
Nucleus of medulla oblongata
Mammillary body
Nucleus of dorsal thalamus
Spinal cord
Septal nuclear complex
Lateral geniculate body
Developmental stage
42-year-old stage
60-year-old stage
50-year-old stage
29-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
7,632 cells
•
Emont et al., 2022
A single-cell atlas of human and mouse white adipose tissue
Explore
h5ad
Mus musculus
Mus musculus
Pericyte
+3
Pericyte
Periovarian fat pad
+2
Periovarian fat pad
19-week-old stage
19-week-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Pericyte
Endothelial cell of lymphatic vessel
Smooth muscle cell
Endothelial cell
Tissue
Periovarian fat pad
Inguinal fat pad
Epididymal fat pad
Developmental stage
19-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
BroadInstitute Single-Cell Portal:SCP1376
gitlab.com
GEO series:GSE176067
GEO series:GSE176171
dbGaP Study:phs002766
Bgee
7,631 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Macaca mulatta (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Macaca mulatta (h5ad)
Macaca mulatta
Macaca mulatta
Sertoli cell
+7
Sertoli cell
Testis
Testis
Normal
Normal
Male
Male
10x genomics v2
10x genomics v2
Organism
Macaca mulatta
Cell type
Sertoli cell
Obsolete somatic cell
Late spermatid
Cell
Spermatocyte
Spermatogonium
Male germ line stem cell
Early spermatid
Tissue
Testis
Developmental stage
Disease
Normal
Sex
Male
Technology
10x genomics v2
Suspension type
Related Links
ebi.ac.uk
Single Cell Portal
7,626 cells
Explore
Mus musculus
Mus musculus
Astrocyte
+5
Astrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Astrocyte
Obsolete excitatory neuron
Microglial cell
Oligodendrocyte precursor cell
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD716) (section 229)
Corresponding registered brain section (MD716) (section 230)
Corresponding registered brain section (MD716) (section 231)
Corresponding registered brain section (MD716) (section 232)
Corresponding registered brain section (MD716) (section 233)
Corresponding registered brain section (MD716) (section 234)
CELLxGENE
7,622 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
GEO series:GSE197353
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
CELLxGENE
7,618 cells
•
Nascimento et al., 2023
Protracted neuronal recruitment in the temporal lobes of young children
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
+9
Oligodendrocyte
Entorhinal cortex
Entorhinal cortex
Newborn stage (0-28 days)
Newborn stage (0-28 days)
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte
Astrocyte
Leukocyte
Microglial cell
Oligodendrocyte precursor cell
Ependymal cell
Gabaergic interneuron
Brain vascular cell
Glutamatergic neuron
Radial glial cell
Tissue
Entorhinal cortex
Developmental stage
Newborn stage (0-28 days)
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE199762
dbGaP Study:phs003509
CELLxGENE
7,594 cells
•
Gupta et al., 2023
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Explore
h5ad
Homo sapiens
Homo sapiens
Brown preadipocyte
+1
Brown preadipocyte
Brown preadipocyte
Brown preadipocyte
56-year-old stage
56-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Brown preadipocyte
Brown adipocyte
Tissue
Brown preadipocyte
Developmental stage
56-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
link.springer.com
dbGaP Study:phs002461
Github:streetslab/Adipogenesis_time_course
CELLxGENE
7,589 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
Schwann cell
+4
Schwann cell
Enteric ganglion
+1
Enteric ganglion
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Schwann cell
Migratory neural crest cell
Enteric neuron
Neural crest cell
Premigratory neural crest cell
Tissue
Enteric ganglion
Neural crest
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
GEO series:GSE295164
CELLxGENE
7,578 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
Lens fiber cell
+2
Lens fiber cell
Lens of camera-type eye
+1
Lens of camera-type eye
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Lens fiber cell
Ectodermal cell
Lens epithelial cell
Tissue
Lens of camera-type eye
Lens vesicle
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
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
7,571 cells
•
Jones et al., 2024
Cellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencing
Explore
h5ad
Homo sapiens
Homo sapiens
Leukocyte
+3
Leukocyte
Ovary
Ovary
28-year-old stage
28-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Leukocyte
Pericyte
Stromal cell of ovary
Endothelial cell
Tissue
Ovary
Developmental stage
28-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE260685
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