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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
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
Double negative thymocyte
+12
Double negative thymocyte
Thymus
Thymus
6-week-old stage
+5
6-week-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Double negative thymocyte
Thymic macrophage
Cd8-positive, alpha-beta thymocyte
B cell
Gamma-delta t cell
Mature cd8 single-positive thymocyte
Leukocyte
Natural killer cell
Erythrocyte
Mature cd4 single-positive thymocyte
Cd4-positive, alpha-beta thymocyte
Double-positive blast
Double-positive, alpha-beta thymocyte
Tissue
Thymus
Developmental stage
6-week-old stage
5-week-old stage
7-week-old stage
4-week-old stage
10-week-old stage
24-day-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE186078
Github:YosefLab/Thymus_CITE-seq
s133.cs.berkeley.edu
s133.cs.berkeley.edu
Zenodo record:8102050
CELLxGENE
71,874 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+11
Fibroblast
Cerebellar vermis
Cerebellar vermis
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular associated smooth muscle cell
Bergmann glial cell
Pericyte
Leukocyte
Ependymal cell
Central nervous system macrophage
Neuron
Endothelial cell
Tissue
Cerebellar vermis
Developmental stage
42-year-old stage
50-year-old stage
29-year-old stage
Disease
Normal
Sex
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
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
Primitive red blood cell
+76
Primitive red blood cell
Lung
Lung
Carnegie stage 19
+7
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Primitive red blood cell
Schwann cell
Common myeloid progenitor
Neural progenitor cell
Cd16-positive, cd56-dim natural killer cell, human
Mast cell
Large pre-b-ii cell
Dendritic cell, human
Bronchus fibroblast of lung
Group 2 innate lymphoid cell
Vein endothelial cell
Early lymphoid progenitor
Smooth muscle cell
Basophil
Lung secretory cell
Neutrophil
Pro-b cell
B-1b b cell
Small pre-b-ii cell
Immature b cell
Dendritic cell
Regulatory t cell
Immature schwann cell
Mesenchymal cell
Bone marrow cell
T-helper 17 cell
Chondrocyte
Tracheobronchial smooth muscle cell
Megakaryocyte
Vascular associated smooth muscle cell
Pre-b-i cell
Fibroblast of lung
Capillary endothelial cell
Pericyte
Late pro-b cell
Epithelial cell of lung
Myofibroblast cell
Club cell
Cd34-positive, cd56-positive, cd117-positive common innate lymphoid precursor, human
Respiratory tract epithelial cell
Hematopoietic stem cell
Non-classical monocyte
Precursor b cell
Pulmonary alveolar type 2 cell
Plasmacytoid dendritic cell
Eosinophil
Cd8-positive, alpha-beta t cell
Promonocyte
Megakaryocyte-erythroid progenitor cell
Pulmonary alveolar type 1 cell
Endothelial cell of lymphatic vessel
Cd16-negative, cd56-bright natural killer cell, human
Granulocyte monocyte progenitor cell
Natural killer cell
Macrophage
Platelet
Erythroblast
Reticulocyte
Schwann cell precursor
Erythrocyte
B-1a b cell
Group 3 innate lymphoid cell
Thymocyte
Pulmonary interstitial fibroblast
Squamous epithelial cell
Mature nk t cell
Basal cell
Classical monocyte
Mesothelial cell
Promyelocyte
Cd4-positive, alpha-beta t cell
T cell
Lung multiciliated epithelial cell
Neuron
Pulmonary neuroendocrine cell
Endothelial cell
Endothelial cell of artery
Tissue
Lung
Developmental stage
Carnegie stage 19
20th week post-fertilization stage
15th week post-fertilization stage
11th week post-fertilization stage
22nd week post-fertilization stage
18th week post-fertilization stage
9th 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-11267
ArrayExpress BioStudies:E-MTAB-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
ArrayExpress BioStudies:E-MTAB-11278
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
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
14-month-old stage
+3
14-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
Hematopoietic precursor cell
Plasma cell
Immature b cell
Mature t cell
Plasmacytoid dendritic cell
Erythroid lineage cell
Granulocyte monocyte progenitor cell
Natural killer cell
Mature b cell
Pro-t cell
Conventional dendritic cell
Thymocyte
Monocyte
Tissue
Thymus
Developmental stage
14-month-old stage
10-month-old stage
5-month-old stage
6-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
Fibroblast
+10
Fibroblast
Ascending aorta
Ascending aorta
53-year-old stage
+9
53-year-old stage
Aortic aneurysm
+1
Aortic aneurysm
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Vascular associated smooth muscle cell
Pericyte
Lymphocyte
Leukocyte
Adipocyte
Endothelial cell of lymphatic vessel
Macrophage
Mesothelial cell
Neuron
Endothelial cell
Tissue
Ascending aorta
Developmental stage
53-year-old stage
52-year-old stage
40-year-old stage
55-year-old stage
58-year-old stage
64-year-old stage
69-year-old stage
63-year-old stage
56-year-old stage
71-year-old stage
Disease
Aortic aneurysm
Normal
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
Fibroblast
+8
Fibroblast
Meninx
+2
Meninx
Carnegie stage 20
+8
Carnegie stage 20
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Mesenchyme condensation cell
Leptomeningeal cell
Fibroblast of choroid plexus
Mesenchymal cell
Chondrocyte
Circulating fibrocyte
Mesothelial cell of dura mater
Arachnoid barrier cell
Tissue
Meninx
Brain meninx
Forebrain meninges
Developmental stage
Carnegie stage 20
Carnegie stage 18
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 23
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
71,183 cells
•
Yao et al., 2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Explore
h5ad
Mus musculus
Mus musculus
Astrocyte
+8
Astrocyte
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
Astrocyte
Leptomeningeal cell
Gabaergic neuron
Smooth muscle cell
Oligodendrocyte precursor cell
Oligodendrocyte
Glutamatergic neuron
Macrophage
Endothelial 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
h5ad
Homo sapiens
Homo sapiens
Stromal cell of endometrium
+6
Stromal cell of endometrium
Endometrium
Endometrium
Young adult stage
Young adult stage
Normal
Normal
Female
Female
10x genomics v3
10x genomics v3
Organism
Homo sapiens
Cell type
Stromal cell of endometrium
Epithelial cell of uterus
Uterine smooth muscle cell
Endothelial cell of uterus
Lymphocyte
Macrophage
Ciliated epithelial 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
8-week-old stage
+1
8-week-old stage
Peripheral neuropathy, non-human animal
+1
Peripheral neuropathy, non-human animal
Female
+1
Female
10x 3' transcription profiling
+6
10x 3' transcription profiling
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
8-week-old stage
15-month-old stage
Disease
Peripheral neuropathy, non-human animal
Normal
Sex
Female
Male
Technology
10x 3' transcription profiling
10x multiome
10x 3' v3
Smart-seq3
Indrop
Smart-seq2
10x 3' v2
Suspension type
Nucleus
Cell
Related Links
DOI:10.3389/fnmol.2022.1038539
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/fncel.2022.885569
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
8-week-old stage
+1
8-week-old stage
Peripheral neuropathy, non-human animal
+1
Peripheral neuropathy, non-human animal
Female
+1
Female
10x 3' transcription profiling
+6
10x 3' transcription profiling
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
8-week-old stage
15-month-old stage
Disease
Peripheral neuropathy, non-human animal
Normal
Sex
Female
Male
Technology
10x 3' transcription profiling
10x multiome
10x 3' v3
Smart-seq3
Indrop
Smart-seq2
10x 3' v2
Suspension type
Nucleus
Cell
Related Links
DOI:10.3389/fnmol.2022.1038539
DOI:10.3389/fncel.2022.885569
DOI:10.1016/j.neuron.2022.03.003
DOI:10.1016/j.neuron.2020.07.026
DOI:10.1038/s41422-021-00479-9
DOI:10.7554/eLife.68457
DOI:10.1016/j.celrep.2021.109914
DOI:10.1038/s41586-019-1900-1
DOI:10.1371/journal.pone.0185543
DOI:10.7554/eLife.76063
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
8-week-old stage
+1
8-week-old stage
Peripheral neuropathy, non-human animal
+1
Peripheral neuropathy, non-human animal
Female
+1
Female
10x 3' transcription profiling
+6
10x 3' transcription profiling
Nucleus
+1
Nucleus
Organism
Mus musculus
Cell type
Sensory neuron of dorsal root ganglion
Tissue
Dorsal root ganglion
Developmental stage
8-week-old stage
15-month-old stage
Disease
Peripheral neuropathy, non-human animal
Normal
Sex
Female
Male
Technology
10x 3' transcription profiling
10x multiome
10x 3' v3
Smart-seq3
Indrop
Smart-seq2
10x 3' v2
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:10.1038/s41422-021-00479-9
DOI:10.7554/eLife.68457
DOI:10.7554/eLife.76063
DOI:10.1016/j.celrep.2021.109914
DOI:10.1016/j.neuron.2020.07.026
DOI:10.1038/s41586-019-1900-1
CELLxGENE
70,803 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Glioblast
+2
Glioblast
Midbrain
+7
Midbrain
10th week post-fertilization stage
+4
10th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glioblast
Oligodendrocyte precursor cell
Radial glial cell
Tissue
Midbrain
Brain
Pons
Cerebellum
Telencephalon
Diencephalon
Hindbrain
Medulla oblongata
Developmental stage
10th week post-fertilization stage
Embryonic stage
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
EGA Study:EGAS00001007472
Github:linnarsson-lab/fetal_brain_multiomics
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