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Cell
896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
125,289 cells
•
Litviňuková et al., 2020
Cells of the adult human heart
Explore
h5ad
Homo sapiens
Homo sapiens
Regular ventricular cardiac myocyte
Regular ventricular cardiac myocyte
Heart right ventricle
+3
Heart right ventricle
Sixth decade stage
+3
Sixth decade stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Regular ventricular cardiac myocyte
Tissue
Heart right ventricle
Apex of heart
Heart left ventricle
Interventricular septum
Developmental stage
Sixth decade stage
Fifth decade stage
Seventh decade stage
Eighth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
ENA Project:ERP123138
support.10xgenomics.com
UCSC Genome Browser:hgTrackUi?db=hg38&g=heartCellAtlas&position=default
Teichmann lab
Github:cartal/HCA_Heart
heartcellatlas.org
UCSC Cell Browser:heart-cell-atlas
HumanCellAtlas:ad98d3cd-26fb-4ee3-99c9-8a2ab085e737
CELLxGENE
125,117 cells
•
Liu et al., 2021
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Granulocyte
+9
Granulocyte
Blood
Blood
66-year-old stage
+31
66-year-old stage
Covid-19
+1
Covid-19
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Granulocyte
Natural killer cell
Platelet
Classical monocyte
Intermediate monocyte
Plasmacytoid dendritic cell
Cd16-positive, cd56-dim natural killer cell, human
Conventional dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Non-classical monocyte
Tissue
Blood
Developmental stage
66-year-old stage
37-year-old stage
71-year-old stage
53-year-old stage
61-year-old stage
52-year-old stage
54-year-old stage
30-year-old stage
55-year-old stage
84-year-old stage
50-year-old stage
51-year-old stage
57-year-old stage
74-year-old stage
49-year-old stage
24-year-old stage
35-year-old stage
58-year-old stage
59-year-old stage
67-year-old stage
32-year-old stage
77-year-old stage
45-year-old stage
70-year-old stage
60-year-old stage
78-year-old stage
63-year-old stage
47-year-old stage
76-year-old stage
79-year-old stage
73-year-old stage
40-year-old stage
Disease
Covid-19
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
John Tsang group
Github:niaid/covid19-time-resolved
GEO series:GSE161918
UCSC Cell Browser:covid19-fatal
HumanCellAtlas:ae62bb31-55ca-4127-b0fb-b1771a604645
CELLxGENE
124,917 cells
•
Nascimento et al., 2023
Protracted neuronal recruitment in the temporal lobes of young children
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
+9
Glutamatergic neuron
Entorhinal cortex
+1
Entorhinal cortex
13-year-old stage
+10
13-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glutamatergic neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Inhibitory interneuron
Brain vascular cell
Ependymal cell
Microglial cell
Astrocyte
Neural progenitor cell
Cortical interneuron
Tissue
Entorhinal cortex
Ganglionic eminence
Developmental stage
13-year-old stage
21st week post-fertilization stage
2-year-old stage
50-year-old stage
51-year-old stage
2-month-old stage
3-year-old stage
1-month-old stage
Newborn stage (0-28 days)
79-year-old stage
27-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
dbGaP Study:phs003509
GEO series:GSE199762
CELLxGENE
124,440 cells
•
Xu et al., 2023
Automatic cell-type harmonization and integration across Human Cell Atlas datasets
Explore
h5ad
Homo sapiens
Homo sapiens
Central memory cd4-positive, alpha-beta t cell
+27
Central memory cd4-positive, alpha-beta t cell
Bronchopulmonary lymph node
+3
Bronchopulmonary lymph node
65-year-old stage
+6
65-year-old stage
Normal
Normal
Female
+1
Female
10x 5' v2
+3
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Central memory cd4-positive, alpha-beta t cell
T cell
Germinal center b cell
Dendritic cell, human
Stromal cell
Endothelial cell of lymphatic vessel
Activated cd4-positive, alpha-beta t cell
Endothelial cell
Mast cell
Effector memory cd4-positive, alpha-beta t cell
Classical monocyte
Plasmacytoid dendritic cell
Macrophage
Memory b cell
Cd16-positive, cd56-dim natural killer cell, human
Innate lymphoid cell
Regulatory t cell
Plasmablast
Plasma cell
T follicular helper cell
B cell
Mucosal invariant t cell
Central memory cd8-positive, alpha-beta t cell
Naive b cell
Conventional dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Effector memory cd8-positive, alpha-beta t cell
Non-classical monocyte
Tissue
Bronchopulmonary lymph node
Thoracic lymph node
Lymph node
Mesenteric lymph node
Developmental stage
65-year-old stage
Sixth decade stage
52-year-old stage
Fifth decade stage
Third decade stage
Seventh decade stage
Eighth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
ebi.ac.uk
EGA dataset:EGAD00001008575
celltypist.org
Github:ventolab/CVID
teichlab.org
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
+8
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
10x gene expression flex
Parse evercode whole transcriptome v2
10x 3' v3
Suspension type
Cell
Related Links
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
Github:danledinh/scRNAseq-repo
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:linnarsson-lab/developing-human-brain?tab=readme-ov-file
EGA dataset: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
ncbi.nlm.nih.gov
morriseylunglab.org
Github:jdplaner/flu_lineage_trace
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
DOI:10.17504/protocols.io.pjvdkn6
DOI:10.17504/protocols.io.bcbrism6
NeMo archive:dat-ch1nqb7
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
Cell
+1
Cell
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
Cell
Nucleus
Related Links
ebi.ac.uk
EGA dataset:EGAD00001008575
celltypist.org
Github:ventolab/CVID
teichlab.org
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.org:#!Synapse:syn45351388/wiki/622682
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