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890
Nucleus
655
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Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
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Most cells
Fewest cells
2328
datasets
CELLxGENE
72,042 cells
•
Steier et al., 2023
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment
Explore
h5ad
Mus musculus
Mus musculus
Thymic macrophage
+12
Thymic macrophage
Thymus
Thymus
7-week-old stage
+5
7-week-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Thymic macrophage
Cd8-positive, alpha-beta thymocyte
Double-positive, alpha-beta thymocyte
Leukocyte
Double-positive blast
Mature cd4 single-positive thymocyte
Cd4-positive, alpha-beta thymocyte
Double negative thymocyte
B cell
Erythrocyte
Mature cd8 single-positive thymocyte
Natural killer cell
Gamma-delta t cell
Tissue
Thymus
Developmental stage
7-week-old stage
10-week-old stage
24-day-old stage
4-week-old stage
5-week-old stage
6-week-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE186078
Github:YosefLab/Thymus_CITE-seq
Zenodo record:8102050
s133.cs.berkeley.edu
s133.cs.berkeley.edu
CELLxGENE
71,874 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+11
Astrocyte
Cerebellar vermis
Cerebellar vermis
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Bergmann glial cell
Vascular associated smooth muscle cell
Fibroblast
Ependymal cell
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Cerebellar vermis
Developmental stage
50-year-old stage
42-year-old stage
29-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
71,752 cells
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Bronchus fibroblast of lung
+76
Bronchus fibroblast of lung
Lung
Lung
9th week post-fertilization stage
+7
9th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Bronchus fibroblast of lung
Myofibroblast cell
Pro-b cell
Common myeloid progenitor
Promonocyte
Schwann cell
Pulmonary interstitial fibroblast
Pulmonary alveolar type 1 cell
Capillary endothelial cell
Classical monocyte
Endothelial cell of lymphatic vessel
Cd4-positive, alpha-beta t cell
Pulmonary alveolar type 2 cell
B-1a b cell
Club cell
Pulmonary neuroendocrine cell
Platelet
Non-classical monocyte
Large pre-b-ii cell
Macrophage
Mesothelial cell
Granulocyte monocyte progenitor cell
Late pro-b cell
Promyelocyte
Mast cell
Tracheobronchial smooth muscle cell
Basal cell
Small pre-b-ii cell
Megakaryocyte-erythroid progenitor cell
Cd16-negative, cd56-bright natural killer cell, human
Epithelial cell of lung
Neutrophil
B-1b b cell
Megakaryocyte
Immature schwann cell
Neural progenitor cell
Immature b cell
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Schwann cell precursor
Reticulocyte
Vein endothelial cell
Dendritic cell, human
Primitive red blood cell
Vascular associated smooth muscle cell
Early lymphoid progenitor
Group 3 innate lymphoid cell
Hematopoietic stem cell
T-helper 17 cell
Pericyte
Endothelial cell
Bone marrow cell
Mesenchymal cell
Erythroblast
Thymocyte
Cd8-positive, alpha-beta t cell
Group 2 innate lymphoid cell
Squamous epithelial cell
Dendritic cell
Erythrocyte
Regulatory t cell
Mature nk t cell
T cell
Plasmacytoid dendritic cell
Precursor b cell
Fibroblast of lung
Smooth muscle cell
Basophil
Neuron
Eosinophil
Lung secretory cell
Cd34-positive, cd56-positive, cd117-positive common innate lymphoid precursor, human
Natural killer cell
Chondrocyte
Endothelial cell of artery
Cd16-positive, cd56-dim natural killer cell, human
Pre-b-i cell
Tissue
Lung
Developmental stage
9th week post-fertilization stage
11th week post-fertilization stage
20th week post-fertilization stage
15th week post-fertilization stage
22nd week post-fertilization stage
Carnegie stage 19
18th week post-fertilization stage
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11267
CELLxGENE
71,732 cells
•
Lavaert et al., 2020
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Explore
h5ad
Homo sapiens
Homo sapiens
Pre-conventional dendritic cell
+13
Pre-conventional dendritic cell
Thymus
Thymus
6-month-old stage
+3
6-month-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Pre-conventional dendritic cell
Mature b cell
Granulocyte monocyte progenitor cell
Erythroid lineage cell
Monocyte
Immature b cell
Conventional dendritic cell
Hematopoietic precursor cell
Thymocyte
Pro-t cell
Plasma cell
Plasmacytoid dendritic cell
Natural killer cell
Mature t cell
Tissue
Thymus
Developmental stage
6-month-old stage
14-month-old stage
5-month-old stage
10-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE144870
HumanCellAtlas:dbd836cf-bfc2-41f0-9834-41cc6c0b235a
CELLxGENE
71,689 cells
•
Chou et al., 2022
Aortic Cellular Diversity and Quantitative Genome-Wide Association Study Trait Prioritization Through Single-Nuclear RNA Sequencing of the Aneurysmal Human Aorta
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+10
Endothelial cell of lymphatic vessel
Ascending aorta
Ascending aorta
52-year-old stage
+9
52-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Leukocyte
Lymphocyte
Macrophage
Mesothelial cell
Adipocyte
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Endothelial cell
Neuron
Tissue
Ascending aorta
Developmental stage
52-year-old stage
64-year-old stage
40-year-old stage
71-year-old stage
63-year-old stage
56-year-old stage
58-year-old stage
53-year-old stage
69-year-old stage
55-year-old stage
Disease
Normal
Aortic aneurysm
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
BroadInstitute Single-Cell Portal:SCP1909
GEO series:GSE207784
CELLxGENE
71,657 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Circulating fibrocyte
+8
Circulating fibrocyte
Meninx
+2
Meninx
9th week post-fertilization stage
+8
9th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Circulating fibrocyte
Fibroblast of choroid plexus
Arachnoid barrier cell
Leptomeningeal cell
Fibroblast
Mesenchymal cell
Chondrocyte
Mesothelial cell of dura mater
Mesenchyme condensation cell
Tissue
Meninx
Brain meninx
Forebrain meninges
Developmental stage
9th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 23
Carnegie stage 21
Carnegie stage 20
Carnegie stage 18
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
71,492 cells
•
Fachrul et al., 2026
Ancestral and environmental diversity shape the immune landscape in Indonesia
Explore
h5ad
Homo sapiens
Homo sapiens
Platelet
+7
Platelet
Blood
Blood
19-year-old stage
+40
19-year-old stage
Normal
Normal
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Platelet
Cd14-positive, cd16-positive monocyte
Monocyte
Megakaryocyte
Cd14-positive monocyte
Conventional dendritic cell
B cell
Plasmacytoid dendritic cell
Tissue
Blood
Developmental stage
19-year-old stage
18-year-old stage
21-year-old stage
32-year-old stage
50-year-old stage
57-year-old stage
46-year-old stage
52-year-old stage
60-year-old stage
22-year-old stage
44-year-old stage
48-year-old stage
45-year-old stage
25-year-old stage
33-year-old stage
40-year-old stage
27-year-old stage
23-year-old stage
37-year-old stage
28-year-old stage
36-year-old stage
54-year-old stage
20-year-old stage
47-year-old stage
31-year-old stage
58-year-old stage
34-year-old stage
51-year-old stage
49-year-old stage
42-year-old stage
35-year-old stage
53-year-old stage
30-year-old stage
24-year-old stage
26-year-old stage
39-year-old stage
43-year-old stage
29-year-old stage
38-year-old stage
41-year-old stage
55-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
Suspension type
Cell
CELLxGENE
71,183 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
+8
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Glutamatergic neuron
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Gabaergic neuron
Macrophage
Leptomeningeal cell
Endothelial cell
Smooth muscle cell
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
DOI:10.17504/protocols.io.pjvdkn6
NeMo archive:dat-ch1nqb7
DOI:10.17504/protocols.io.bcbrism6
Bgee
71,032 cells
•
Wang et al., 2020
Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle
Explore
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Homo sapiens (h5ad)
Homo sapiens
Homo sapiens
Ciliated epithelial cell
+6
Ciliated epithelial cell
Endometrium
Endometrium
Young adult stage
Young adult stage
Normal
Normal
Female
Female
10x genomics v3
10x genomics v3
Organism
Homo sapiens
Cell type
Ciliated epithelial cell
Lymphocyte
Macrophage
Endothelial cell of uterus
Stromal cell of endometrium
Epithelial cell of uterus
Uterine smooth muscle cell
Tissue
Endometrium
Developmental stage
Young adult stage
Disease
Normal
Sex
Female
Technology
10x genomics v3
Suspension type
Related Links
SRA Project:SRP135922
CELLxGENE
70,963 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
Sensory neuron of dorsal root ganglion
Sensory neuron of dorsal root ganglion
Dorsal root ganglion
Dorsal root ganglion
15-month-old stage
+1
15-month-old stage
Normal
+1
Normal
Female
+1
Female
Smart-seq2
+6
Smart-seq2
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
15-month-old stage
8-week-old stage
Disease
Normal
Peripheral neuropathy, non-human animal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v3
Indrop
Smart-seq3
10x multiome
10x 3' v2
10x 3' transcription profiling
Suspension type
Nucleus
Cell
Related Links
DOI:10.3389/fnmol.2022.1038539
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:10.1038/s41422-021-00479-9
CELLxGENE
70,963 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
Sensory neuron of dorsal root ganglion
Sensory neuron of dorsal root ganglion
Dorsal root ganglion
Dorsal root ganglion
15-month-old stage
+1
15-month-old stage
Normal
+1
Normal
Female
+1
Female
Smart-seq2
+6
Smart-seq2
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
15-month-old stage
8-week-old stage
Disease
Normal
Peripheral neuropathy, non-human animal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v3
Indrop
Smart-seq3
10x multiome
10x 3' v2
10x 3' transcription profiling
Suspension type
Nucleus
Cell
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
70,963 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
Sensory neuron of dorsal root ganglion
Sensory neuron of dorsal root ganglion
Dorsal root ganglion
Dorsal root ganglion
15-month-old stage
+1
15-month-old stage
Normal
+1
Normal
Female
+1
Female
Smart-seq2
+6
Smart-seq2
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
15-month-old stage
8-week-old stage
Disease
Normal
Peripheral neuropathy, non-human animal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v3
Indrop
Smart-seq3
10x multiome
10x 3' v2
10x 3' transcription profiling
Suspension type
Nucleus
Cell
Related Links
DOI:10.3389/fnmol.2022.1038539
DOI:10.3389/fncel.2022.885569
DOI:10.1371/journal.pone.0185543
DOI:10.1016/j.neuron.2020.07.026
DOI:10.1038/s41422-021-00479-9
DOI:10.7554/eLife.68457
DOI:10.7554/eLife.76063
DOI:10.1038/s41586-019-1900-1
DOI:10.1016/j.neuron.2022.03.003
DOI:10.1016/j.celrep.2021.109914
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