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Nucleus
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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
CELLxGENE
124,252 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+7
Neutrophil
Aorta
Aorta
15-week-old stage
+6
15-week-old stage
Atherosclerosis
Atherosclerosis
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Neutrophil
Endothelial cell
Microvascular endothelial cell
Smooth muscle cell
Lymphocyte
Macrophage
Neuron
Fibroblast
Tissue
Aorta
Developmental stage
15-week-old stage
13-week-old stage
24-week-old stage
20-week-old stage
11-week-old stage
17-week-old stage
8-week-old stage
Disease
Atherosclerosis
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE321762
CELLxGENE
124,132 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+8
Natural killer cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
Bd rhapsody whole transcriptome analysis
+7
Bd rhapsody whole transcriptome analysis
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Cytotoxic t cell
Plasmacytoid dendritic cell
Cd4-positive, alpha-beta t cell
Cd14-positive monocyte
Megakaryocyte
Cd14-low, cd16-positive monocyte
B cell
Dendritic cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
Bd rhapsody whole transcriptome analysis
10x 5' v2
Particle-templated instant partition sequencing
Asteria scrna-seq kit
Scalebio single cell rna sequencing
Hive clx single-cell rnaseq solution
Parse evercode whole transcriptome v2
10x 3' v3
Suspension type
Cell
Related Links
github.com
PRJNA1106903
zenodo.org
CELLxGENE
123,236 cells
•
Mossi Albiach et al., 2023
Futile wound healing drives mesenchymal-like cell phenotypes in human glioblastoma
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
+12
Oligodendrocyte precursor cell
Right temporal lobe
Right temporal lobe
63-year-old stage
63-year-old stage
Glioblastoma
Glioblastoma
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Lymphocyte
Macrophage
Microglial cell
Neoplastic cell
Pericyte
Myeloid leukocyte
Monocyte
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Right temporal lobe
Developmental stage
63-year-old stage
Disease
Glioblastoma
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
123,161 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Glioblast
+5
Glioblast
Medulla oblongata
Medulla oblongata
14th week post-fertilization stage
+4
14th week post-fertilization stage
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Glioblast
Oligodendrocyte
Neuroblast (sensu nematoda and protostomia)
Neuroblast (sensu vertebrata)
Radial glial cell
Neuron
Tissue
Medulla oblongata
Developmental stage
14th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 18
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github
EGAD00001006049
CELLxGENE
123,154 cells
•
Niethamer et al., 2025
Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states
Explore
h5ad
Mus musculus
Mus musculus
T cell
+26
T cell
Middle lobe of right lung
Middle lobe of right lung
9-week-old stage
+9
9-week-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Neutrophil
Mature conventional dendritic cell
Ciliated cell
Natural killer cell
Pulmonary alveolar epithelial cell
Secretory cell
Lung interstitial macrophage
Alveolar capillary type 1 endothelial cell
Endothelial cell of respiratory system lymphatic vessel
Endothelial cell of artery
Classical monocyte
Mesothelial cell of pleura
Pulmonary alveolar type 1 cell
Fibroblast of lung
Alveolar macrophage
Plasma cell
Vein endothelial cell
Alveolar adventitial fibroblast
B cell
Alveolar capillary type 2 endothelial cell
Alveolar type 1 fibroblast cell
Vascular associated smooth muscle cell
Conventional dendritic cell
Adventitial fibroblast
Pulmonary alveolar type 2 cell
Non-classical monocyte
Tissue
Middle lobe of right lung
Developmental stage
9-week-old stage
14-month-old stage
4-month-old stage
12-week-old stage
3-month-old stage
11-week-old stage
7-week-old stage
5-month-old stage
6-week-old stage
10-week-old stage
Disease
Normal
Influenza
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE262927
morriseylunglab.org
github.com
CELLxGENE
122,641 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
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Glutamatergic neuron
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Macrophage
Astrocyte
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
Methyl-C sequencing of single cell nuclei: snmC-seq2
Fresh Frozen Mouse Brain Preparation (for Single Nuclei Sequencing)
assets.nemoarchive.org
CELLxGENE
121,916 cells
•
Xu et al., 2023
Automatic cell-type harmonization and integration across Human Cell Atlas datasets
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+8
Endothelial cell
Islet of langerhans
+1
Islet of langerhans
53-year-old stage
+14
53-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Nucleus
+1
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell
Pancreatic acinar cell
Pancreatic pp cell
Pancreatic a cell
Macrophage
Pancreatic d cell
Pancreatic stellate cell
Type b pancreatic cell
Pancreatic ductal cell
Tissue
Islet of langerhans
Pancreas
Developmental stage
53-year-old stage
61-year-old stage
54-year-old stage
48-year-old stage
30-year-old stage
39-year-old stage
74-year-old stage
24-year-old stage
23-year-old stage
35-year-old stage
59-year-old stage
77-year-old stage
46-year-old stage
22-year-old stage
63-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Cel-seq2
10x 3' v2
Suspension type
Nucleus
Cell
Related Links
scBS-seq data (PRJEB50820)
Smart-seq2 data, scATAC-seq data and 10x-Genomics Chromium droplet-based scRNA-seq data (EGAD00001008575)
CellTypist webpage
Analysis scripts
Teichmann Lab
Single Cell Portal
121,344 cells
Explore
Homo sapiens
Homo sapiens
Peripheral blood mononuclear cell
Peripheral blood mononuclear cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Homo sapiens
Cell type
Peripheral blood mononuclear cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
120,807 cells
•
Gittings et al., 2023
Cryptic exon detection and transcriptomic changes revealed in single-nuclei RNA sequencing of C9ORF72 patients spanning the ALS-FTD spectrum
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
+5
Oligodendrocyte precursor cell
Occipital cortex
Occipital cortex
66-year-old stage
+14
66-year-old stage
Amyotrophic lateral sclerosis
+2
Amyotrophic lateral sclerosis
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Microglial cell
Neuron
Astrocyte
Tissue
Occipital cortex
Developmental stage
66-year-old stage
43-year-old stage
71-year-old stage
61-year-old stage
54-year-old stage
68-year-old stage
56-year-old stage
50-year-old stage
51-year-old stage
72-year-old stage
58-year-old stage
59-year-old stage
70-year-old stage
47-year-old stage
73-year-old stage
Disease
Amyotrophic lateral sclerosis
Amyotrophic lateral sclerosis 26 with or without frontotemporal dementia
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Synapse
CELLxGENE
120,042 cells
•
Toth et al., 2022
Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates
Explore
h5ad
Macaca mulatta
Macaca mulatta
T cell
+15
T cell
Lung
Lung
Late embryonic stage
Late embryonic stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Macaca mulatta
Cell type
T cell
Club cell
Granulocyte
Multiciliated epithelial cell of the bronchus
Mucosal type mast cell
Platelet
Erythroid lineage cell
Smooth muscle cell
Pulmonary alveolar type 1 cell
Lung endothelial cell
Fibroblast of lung
B cell
Mucosal invariant t cell
Myeloid leukocyte
Dendritic cell
Pulmonary alveolar type 2 cell
Tissue
Lung
Developmental stage
Late embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
ncbi.nlm.nih.gov
Images
LungMAP ShinyCell
LungMAP Portal
ncbi.nlm.nih.gov
Single Cell Portal
119,845 cells
•
Chou et al., 2025
Zinc Finger Repressors mediate widespread <i>PRNP<i> lowering in the nonhuman primate brain and profoundly extend survival in prion disease mice
Explore
scRNAseq_updated.h5ad (h5ad)
Mus musculus
Mus musculus
Cell
+8
Cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Cell
Oligodendrocyte precursor cell
Oligodendrocyte
Brain pericyte
Microglial cell
Endothelial stalk cell
Neuron
Astrocyte
Fibroblast
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
118,925 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Cranial nerve ii
+1
Cranial nerve ii
69-year-old stage
+46
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Cranial nerve ii
Optic disc
Developmental stage
69-year-old stage
37-year-old stage
75-year-old stage
21-year-old stage
34-year-old stage
65-year-old stage
42-year-old stage
43-year-old stage
71-year-old stage
85-year-old stage
53-year-old stage
61-year-old stage
52-year-old stage
54-year-old stage
68-year-old stage
30-year-old stage
17-year-old stage
56-year-old stage
15-year-old stage
82-year-old stage
50-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
16-year-old stage
58-year-old stage
25-year-old stage
67-year-old stage
90 year-old and over stage
3-year-old stage
32-year-old stage
77-year-old stage
33-year-old stage
64-year-old stage
45-year-old stage
62-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
18-year-old stage
Newborn stage (0-28 days)
63-year-old stage
47-year-old stage
76-year-old stage
11-year-old stage
27-year-old stage
10-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
celltype.info
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