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Cell
871
Nucleus
653
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Asap
43
Bgee
40
Cellxgene
2,045
Single cell portal
176
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Most cells
Fewest cells
2304
datasets
CELLxGENE
87,234 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Gabaergic neuron
Gabaergic neuron
Dorsolateral prefrontal cortex
+2
Dorsolateral prefrontal cortex
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Gabaergic neuron
Tissue
Dorsolateral prefrontal cortex
Brodmann (1909) area 25
Prefrontal cortex
Developmental stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:dat-1je0mn3
submit.brainimagelibrary.org
CELLxGENE
87,000 cells
•
Fernandes Matuck et al., 2024
The Immunoregulatory Architecture of the Adult Oral Cavity
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+21
Fibroblast
Soft palate
+4
Soft palate
35-year-old stage
+16
35-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Schwann cell
Keratinocyte
Mast cell
Langerhans cell
Mural cell
Melanocyte
Neutrophil
Plasma cell
Dendritic cell
B cell
Blood vessel endothelial cell
Myoepithelial cell
Merkel cell
Salivary gland glandular cell
Cd4-positive helper t cell
Adult skeletal muscle myoblast
Cd8-positive, alpha-beta t cell
Endothelial cell of lymphatic vessel
Natural killer cell
Macrophage
Acinar cell of salivary gland
Tissue
Soft palate
Hard palate
Buccal mucosa
Gingiva
Mucosa of lip
Developmental stage
35-year-old stage
39-year-old stage
21-year-old stage
61-year-old stage
57-year-old stage
Sixth decade stage
22-year-old stage
51-year-old stage
33-year-old stage
32-year-old stage
28-year-old stage
31-year-old stage
56-year-old stage
24-year-old stage
65-year-old stage
Seventh decade stage
34-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:Loci-lab/Oral-Craniofacial-Atlas
CELLxGENE
85,875 cells
•
Ulrich et al., 2024
Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+5
Fibroblast
Myometrium
+1
Myometrium
26-year-old stage
+7
26-year-old stage
Normal
Normal
Female
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Fibro/adipogenic progenitor cell
Perivascular cell
Decidual cell
Stromal cell of endometrium
Uterine smooth muscle cell
Tissue
Myometrium
Endometrium
Developmental stage
26-year-old stage
23-year-old stage
29-year-old stage
32-year-old stage
28-year-old stage
Young adult stage
31-year-old stage
37-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10287
GEO series:GSE111976
GEO series:GSE260658
CELLxGENE
85,546 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Neuron
Neuron
Intralaminar nuclear group
+27
Intralaminar nuclear group
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
Neuron
Tissue
Intralaminar nuclear group
Primary motor cortex
Dentate gyrus of hippocampal formation
Ventral anterior nucleus of thalamus
Subthalamic nucleus
Globus pallidus
Midbrain tectum
Lateral nuclear group of thalamus
Epithalamus
Medial dorsal nucleus of thalamus
Medial zone of hypothalamus
Lateral geniculate body
Nucleus of dorsal thalamus
Midbrain nucleus
Piriform cortex
Accessory basal amygdaloid nucleus
Hypothalamus
Centromedian nucleus of thalamus
Substantia nigra
Septal nuclear complex
Pulvinar nucleus
Bed nucleus of stria terminalis
Medial geniculate body
Gray matter of midbrain
Anterior nuclear group
Central amygdaloid nucleus
Pretectal region
Lateral posterior nucleus of thalamus
Developmental stage
42-year-old stage
50-year-old stage
29-year-old stage
60-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
85,233 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
Common myeloid progenitor
+21
Common myeloid progenitor
Blood
Blood
61-year-old stage
+6
61-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Common myeloid progenitor
Intermediate monocyte
Myeloid dendritic cell
Hematopoietic precursor cell
Basophil
Neutrophil
Plasma cell
B cell
Regulatory t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Hematopoietic stem cell
Non-classical monocyte
Plasmacytoid dendritic cell
Cd8-positive, alpha-beta t cell
Natural killer cell
Macrophage
Platelet
Erythrocyte
Monocyte
Mature nk t cell
Classical monocyte
Cd4-positive, alpha-beta t cell
Tissue
Blood
Developmental stage
61-year-old stage
45-year-old stage
59-year-old stage
33-year-old stage
69-year-old stage
60-year-old stage
56-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
Smart-seq2
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
Single Cell Portal
84,973 cells
Explore
Mus musculus
Mus musculus
Myeloid cell
+12
Myeloid cell
Fibrotic liver disease
+1
Fibrotic liver disease
10x 3' transcription profiling
10x 3' transcription profiling
Organism
Mus musculus
Cell type
Myeloid cell
Granulocyte
Neutrophil
Stromal cell
Alpha-beta t cell
Plasma cell
B cell
Gamma-delta t cell
Hepatocyte
Plasmacytoid dendritic cell
Natural killer cell
Erythrocyte
Conventional dendritic cell
Tissue
Developmental stage
Disease
Fibrotic liver disease
Normal
Sex
Technology
10x 3' transcription profiling
Suspension type
Related Links
bioRxiv pre-print version of the manuscript
CELLxGENE
84,658 cells
•
Techameena et al., 2024
The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment
Explore
h5ad
Mus musculus
Mus musculus
Fibroblast
+9
Fibroblast
Trigeminal ganglion
Trigeminal ganglion
8-week-old stage
8-week-old stage
Peripheral neuropathy
+1
Peripheral neuropathy
Female
+1
Female
Bd rhapsody whole transcriptome analysis
+4
Bd rhapsody whole transcriptome analysis
Cell
+1
Cell
Organism
Mus musculus
Cell type
Fibroblast
Glial cell
Smooth muscle cell
Neutrophil
B cell
Pericyte
Trigeminal neuron
Macrophage
Connective tissue cell
Endothelial cell
Tissue
Trigeminal ganglion
Developmental stage
8-week-old stage
Disease
Peripheral neuropathy
Normal
Sex
Female
Male
Technology
Bd rhapsody whole transcriptome analysis
10x 3' v3
Smart-seq3
Drop-seq
Indrop
Suspension type
Cell
Nucleus
Related Links
DOI:10.3389/fncel.2022.885569
DOI:10.1371/journal.pone.0185543
DOI:10.1016/j.neuron.2022.03.003
DOI:10.1016/j.neuron.2020.07.026
DOI:10.7554/eLife.68457
DOI:10.7554/eLife.76063
DOI:10.1016/j.celrep.2021.109914
DOI:10.1038/s41586-019-1900-1
DOI:10.3389/fnmol.2022.1038539
DOI:10.1038/s41422-021-00479-9
CELLxGENE
83,731 cells
•
Lazarescu et al., 2025
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
Explore
h5ad
Homo sapiens
Homo sapiens
Mast cell
+11
Mast cell
Visceral fat
Visceral fat
Adult stage
+8
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mast cell
Myeloid lineage restricted progenitor cell
Mural cell
B cell
Adipocyte of omentum tissue
Endothelial cell of lymphatic vessel
Macrophage
Mesenchymal stem cell of adipose tissue
Monocyte
Mesothelial cell
T cell
Endothelial cell
Tissue
Visceral fat
Developmental stage
Adult stage
53-year-old stage
48-year-old stage
41-year-old stage
29-year-old stage
33-year-old stage
28-year-old stage
24-year-old stage
34-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE281356
DOI:10.5281/zenodo.14001210
HumanCellAtlas:df8eb7ce-3707-46af-b823-e081a562e954
CELLxGENE
83,674 cells
•
Tian et al., 2023
Single-cell DNA methylation and 3D genome architecture in the human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+6
Astrocyte
Primary motor cortex
+16
Primary motor cortex
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
Snm3c-seq
Snm3c-seq
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Cell
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular leptomeningeal cell
Macroglial cell
Endothelial cell
Tissue
Primary motor cortex
Primary visual cortex
Brodmann (1909) area 46
Globus pallidus
Nucleus accumbens
Putamen
Amygdala
Corticomedial nuclear complex
Piriform cortex
Brodmann (1909) area 24
Lateral entorhinal cortex
Septal nuclear complex
Middle temporal gyrus
Agranular insular cortex
Body of caudate nucleus
Substantia innominata
Bed nucleus of stria terminalis
Developmental stage
42-year-old stage
58-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
Snm3c-seq
Suspension type
Nucleus
Related Links
GEO series:GSE215353
NeMo archive:dat-jx4eu3g
CELLxGENE
83,674 cells
•
Tian et al., 2023
Single-cell DNA methylation and 3D genome architecture in the human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+6
Astrocyte
Primary motor cortex
+16
Primary motor cortex
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
Snm3c-seq
Snm3c-seq
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Cell
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular leptomeningeal cell
Macroglial cell
Endothelial cell
Tissue
Primary motor cortex
Primary visual cortex
Brodmann (1909) area 46
Globus pallidus
Nucleus accumbens
Putamen
Amygdala
Corticomedial nuclear complex
Piriform cortex
Brodmann (1909) area 24
Lateral entorhinal cortex
Septal nuclear complex
Middle temporal gyrus
Agranular insular cortex
Body of caudate nucleus
Substantia innominata
Bed nucleus of stria terminalis
Developmental stage
42-year-old stage
58-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
Snm3c-seq
Suspension type
Nucleus
Related Links
GEO series:GSE215353
NeMo archive:dat-jx4eu3g
CELLxGENE
83,651 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Vein endothelial cell
+2
Vein endothelial cell
Breast
Breast
Adult stage
+1
Adult stage
Normal
Normal
Female
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Vein endothelial cell
Capillary endothelial cell
Endothelial cell of artery
Tissue
Breast
Developmental stage
Adult stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
GEO series:GSE195665
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
CELLxGENE
83,451 cells
•
Joseph et al., 2021
Single‐cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions
Explore
h5ad
Homo sapiens
Homo sapiens
Secretory cell
+24
Secretory cell
Transition zone of prostate
+1
Transition zone of prostate
73-year-old stage
+7
73-year-old stage
Benign prostatic hyperplasia
+1
Benign prostatic hyperplasia
Male
Male
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Secretory cell
Smooth muscle cell of prostate
Luminal cell of prostate epithelium
Granulocyte
Cd141-positive myeloid dendritic cell
Cd8-positive, alpha-beta thymocyte
Plasma cell
Dendritic cell
B cell
Epithelial cell of urethra
Prostate gland microvascular endothelial cell
Vascular associated smooth muscle cell
Cd1c-positive myeloid dendritic cell
Pericyte
Fibroblast of connective tissue of nonglandular part of prostate
Non-classical monocyte
Plasmacytoid dendritic cell
Basal cell of prostate epithelium
Effector cd8-positive, alpha-beta t cell
Effector cd4-positive, alpha-beta t cell
Natural killer cell
Fibroblast of connective tissue of glandular part of prostate
Cd4-positive, alpha-beta thymocyte
Mature nk t cell
Classical monocyte
Tissue
Transition zone of prostate
Peripheral zone of prostate
Developmental stage
73-year-old stage
74-year-old stage
72-year-old stage
81-year-old stage
29-year-old stage
31-year-old stage
67-year-old stage
71-year-old stage
Disease
Benign prostatic hyperplasia
Normal
Sex
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
DOI:10.25548/17-DRBC
GEO series:GSE172357
strandlab.net
GEO series:GSE173096
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