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Technology
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Cell
934
Nucleus
679
Data Source
0
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
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Most cells
Fewest cells
2515
datasets
ASAP
v8
6,235 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Organism
Microcebus murinus
Cell type
Tissue
Developmental stage
Disease
Sex
Technology
Suspension type
CELLxGENE
6,210 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Liver
Liver
44-year-old stage
44-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Blood vessel endothelial cell
Blood vessel smooth muscle cell
Macrophage
Plasma cell
Malignant cell
Fibroblast
Tissue
Liver
Developmental stage
44-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
phs002371
CELLxGENE
6,201 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+8
Endothelial cell
Pancreas
Pancreas
20-month-old stage and over
+1
20-month-old stage and over
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell
Pancreatic acinar cell
Pancreatic pp cell
Leukocyte
Pancreatic a cell
Pancreatic d cell
Pancreatic stellate cell
Type b pancreatic cell
Pancreatic ductal cell
Tissue
Pancreas
Developmental stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GSE132042
Processed files
Tabula Muris Senis
SmartSeq2 for HTP Generation of FACS Sorted Single Cell Libraries V.1
github.com
CELLxGENE
6,198 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+22
T cell
Ovary
Ovary
12-month-old stage
12-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
T cell
Granulosa cell
Blood vessel endothelial cell
Stromal cell
Endothelial cell of lymphatic vessel
Cumulus granulosa cell
Mast cell
Smooth muscle cell
Steroidogenic stromal cell of ovary
Endothelial cell of vascular tree
Ovarian surface epithelial cell
Adipocyte
Macrophage
Oviduct secretory cell
Plasma cell
Oocyte
Late luteal cell
Atretic granulosa cell
Early luteal cell
Theca cell
Dendritic cell
Ovarian fibroblast
Mural granulosa cell
Tissue
Ovary
Developmental stage
12-month-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
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
Github
EGAD00001006049
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
insitubiology.org
GSE197353
figshare.com
figshare.com
figshare.com
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
Methyl-C sequencing of single cell nuclei: snmC-seq2
Fresh Frozen Mouse Brain Preparation (for Single Nuclei Sequencing)
assets.nemoarchive.org
CELLxGENE
6,154 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+20
T cell
Ovary
Ovary
3-month-old stage
3-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
T cell
Granulosa cell
Blood vessel endothelial cell
Stromal cell
Endothelial cell of lymphatic vessel
Cumulus granulosa cell
Smooth muscle cell
Steroidogenic stromal cell of ovary
Endothelial cell of vascular tree
Ovarian surface epithelial cell
Adipocyte
Macrophage
Oviduct secretory cell
Oocyte
Late luteal cell
Atretic granulosa cell
Early luteal cell
Theca cell
Dendritic cell
Ovarian fibroblast
Mural granulosa cell
Tissue
Ovary
Developmental stage
3-month-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
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.com
explore.data.humancellatlas.org
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
Allen Brain Map
Reference middle temporal gyrus taxonomy
Allen Brain Map Patch-seq
assets.nemoarchive.org
github.com
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
GSE135133
singlecell.broadinstitute.org
explore.data.humancellatlas.org
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
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