Home
Data
Contribute
Stats
Resources
Metadata schema
Tools
Community
About
Contact us
Organism
0
Clear
Cell Type
0
Clear
Tissue
0
Clear
Developmental Stage
0
Clear
Disease
0
Clear
Sex
0
Clear
Technology
0
Clear
Suspension Type
0
Clear
Cell
896
Nucleus
659
Data Source
0
Clear
Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
18,100 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
Photoreceptor cell
Photoreceptor cell
Multicellular anatomical structure
Multicellular anatomical structure
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Photoreceptor cell
Tissue
Multicellular anatomical structure
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
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
GEO series:GSE295164
CELLxGENE
18,011 cells
•
Liang et al., 2023
A multi-omics atlas of the human retina at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal pigment epithelial cell
+3
Retinal pigment epithelial cell
Peripheral region of retina
+2
Peripheral region of retina
65-year-old stage
+4
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Retinal pigment epithelial cell
Microglial cell
Mueller cell
Astrocyte
Tissue
Peripheral region of retina
Macula lutea proper
Fovea centralis
Developmental stage
65-year-old stage
84-year-old stage
78-year-old stage
73-year-old stage
83-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
UCSC Cell Browser:retina-atac
HumanCellAtlas:9c20a245-f2c0-43ae-82c9-2232ec6b594f
GEO series:GSE226108
CELLxGENE
17,962 cells
•
Hochane et al., 2019
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney cell
+9
Kidney cell
Kidney
Kidney
Carnegie stage 19
+4
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Kidney cell
Podocyte
Endothelial cell
Mesonephric nephron tubule epithelial cell
Glomerular mesangial cell
Leukocyte
Epithelial cell of proximal tubule
Kidney connecting tubule epithelial cell
Kidney interstitial cell
Kidney epithelial cell
Tissue
Kidney
Developmental stage
Carnegie stage 19
14th week post-fertilization stage
16th week post-fertilization stage
9th week post-fertilization stage
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE114530
semraulab.com
CELLxGENE
17,909 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Podocyte
+17
Podocyte
Renal medulla
Renal medulla
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Parietal epithelial cell
Endothelial cell
Kidney loop of henle thin descending limb epithelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Kidney inner medulla collecting duct epithelial cell
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule epithelial cell
Urothelial cell
Kidney loop of henle thick ascending limb epithelial cell
Kidney loop of henle epithelial cell
Mesangial cell
Pericyte
Kidney proximal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
64-year-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
CELLxGENE
17,891 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Glutamatergic neuron
Glutamatergic 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
Glutamatergic neuron
Tissue
Hippocampal formation
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
submit.brainimagelibrary.org
NeMo archive:dat-1je0mn3
ASAP
17,868 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Neuron
+19
Neuron
Oenocyte
Oenocyte
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Neuron
Fat cell
Cardial cell
Tracheolar cell
Glial cell
Somatic precursor cell
Male germline cell
Hemocyte
Adult enterocyte
Epithelial cell
Adult alary muscle cell
Muscle cell
Adult tracheocyte
Adult neuron
Sensory neuron
Oenocyte
Adult oenocyte
Motor neuron
Neuron
Female germline cell
Tissue
Oenocyte
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
17,799 cells
•
Jäkel et al., 2019
Altered human oligodendrocyte heterogeneity in multiple sclerosis
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
+10
Oligodendrocyte precursor cell
Brain white matter
+1
Brain white matter
37-year-old stage
+7
37-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Leukocyte
Macrophage
Microglial cell
Pericyte
Progenitor cell
Neuron
Vascular associated smooth muscle cell
Astrocyte
Tissue
Brain white matter
Brain
Developmental stage
37-year-old stage
44-year-old stage
82-year-old stage
57-year-old stage
49-year-old stage
35-year-old stage
64-year-old stage
60-year-old stage
Disease
Normal
Multiple sclerosis
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE118257
EGA Study:EGAS00001003412
ki.se
ENA Project:PRJEB39323
HumanCellAtlas:38449aea-70b5-40db-84b3-1e08f32efe34
CELLxGENE
17,786 cells
•
The Tabula Sapiens Consortium* et al., 2022
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+24
T cell
Skin of abdomen
+3
Skin of abdomen
61-year-old stage
+3
61-year-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Neutrophil
Muscle cell
Stromal cell
Natural killer cell
Erythrocyte
Activated cd4-positive, alpha-beta t cell
Endothelial cell
Mature nk t cell
Mast cell
Cd8-positive, alpha-beta t cell
Melanocyte
Smooth muscle cell
Epithelial cell
Myeloid dendritic cell
Macrophage
Regulatory t cell
Plasma cell
Cd4-positive, alpha-beta t cell
Langerhans cell
B cell
Basophil
Fibroblast
Sebocyte
Keratocyte
Tissue
Skin of abdomen
Skin of body
Buccal mucosa
Skin of chest
Developmental stage
61-year-old stage
59-year-old stage
33-year-old stage
45-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v3
Suspension type
Cell
Related Links
AWS Open Data:tabula-sapiens
CZ BioHub Portal:tabula-sapiens-portal
HumanCellAtlas:10201832-7c73-4033-9b65-3ef13d81656a
UCSC Cell Browser:tabula-sapiens
DOI:10.1101/2024.12.03.626516
UCSC Genome Browser:hgTrackUi?hgsid=1437536541_FfasmBrAlAiA7oFphu1csVv0KHgc&db=hg38&c=chrX&g=tabulaSapiens
CELLxGENE
17,777 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+8
Endothelial cell
Renal medulla
Renal medulla
53-year-old stage
53-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Tissue
Renal medulla
Developmental stage
53-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
CELLxGENE
17,704 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+8
Endothelial cell
Renal medulla
Renal medulla
53-year-old stage
53-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Tissue
Renal medulla
Developmental stage
53-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
17,660 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+18
Midbrain-derived inhibitory neuron
Nucleus of dorsal thalamus
Nucleus of dorsal thalamus
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Microglial cell
Thalamic excitatory neuron
Pericyte
Neuron
Monocyte
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Nucleus of dorsal thalamus
Developmental stage
50-year-old stage
Disease
Normal
Sex
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
17,628 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
+14
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
Anterior visceral endoderm cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
1
2
…
102
103
104
105
106
…
390
391
Close