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Disease
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Technology
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Cell
934
Nucleus
679
Data Source
0
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
Sort
Most cells
Fewest cells
2515
datasets
CELLxGENE
4,154 cells
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Gut endothelial cell
Gut endothelial cell
Hindgut
+2
Hindgut
19th week post-fertilization stage
+11
19th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Gut endothelial cell
Tissue
Hindgut
Ileum
Colon
Developmental stage
19th week post-fertilization stage
21st week post-fertilization stage
23rd week post-fertilization stage
13th week post-fertilization stage
14th week post-fertilization stage
20th week post-fertilization stage
17th week post-fertilization stage
16th week post-fertilization stage
10th week post-fertilization stage
18th week post-fertilization stage
Carnegie stage 22
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE158328
simmonslab.shinyapps.io
Supplementary data
dropbox.com
GSE158702
explore.data.humancellatlas.org
CELLxGENE
4,147 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+8
Neutrophil
Respiratory airway
Respiratory airway
74-year-old stage
74-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Erythrocyte
Mature nk t cell
Mast cell
Platelet
Ionocyte
Epithelial cell
Myeloid cell
B cell
Tissue
Respiratory airway
Developmental stage
74-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
data.mendeley.com
github.com
covid19cellatlas.org
CELLxGENE
4,144 cells
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Neuroendocrine cell
+6
Neuroendocrine cell
Hindgut
+2
Hindgut
19th week post-fertilization stage
+11
19th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neuroendocrine cell
Inhibitory motor neuron
Neural cell
Glial cell
Motor neuron
Interneuron
Progenitor cell
Tissue
Hindgut
Ileum
Colon
Developmental stage
19th week post-fertilization stage
21st week post-fertilization stage
23rd week post-fertilization stage
13th week post-fertilization stage
14th week post-fertilization stage
20th week post-fertilization stage
17th week post-fertilization stage
16th week post-fertilization stage
10th week post-fertilization stage
18th week post-fertilization stage
Carnegie stage 22
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE158328
simmonslab.shinyapps.io
Supplementary data
dropbox.com
GSE158702
explore.data.humancellatlas.org
CELLxGENE
4,142 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Fast muscle cell
+22
Fast muscle cell
Limb muscle
Limb muscle
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Microcebus murinus
Cell type
Fast muscle cell
Neutrophil
Endothelial cell of lymphatic vessel
Slow muscle cell
Reticular cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Tendon cell
Erythroid lineage cell
Endothelial cell of artery
Capillary endothelial cell
Lymphocyte
Adipocyte
Macrophage
Plasma cell
Cd4-positive, alpha-beta t cell
Vein endothelial cell
B cell
Pericyte
Skeletal muscle satellite stem cell
Mesenchymal stem cell
Vascular associated smooth muscle cell
Basophil
Tissue
Limb muscle
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
cells.ucsc.edu
Globus
ASAP
v8
4,142 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Organism
Microcebus murinus
Cell type
Tissue
Developmental stage
Disease
Sex
Technology
Suspension type
CELLxGENE
4,138 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
Small pre-b-ii cell
+8
Small pre-b-ii cell
Lung
Lung
15th week post-fertilization stage
+5
15th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Small pre-b-ii cell
Pro-b cell
Late pro-b cell
Pre-b-i cell
B-1a b cell
Precursor b cell
B-1b b cell
Large pre-b-ii cell
Immature b cell
Tissue
Lung
Developmental stage
15th week post-fertilization stage
20th week post-fertilization stage
9th week post-fertilization stage
18th week post-fertilization stage
22nd week post-fertilization stage
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
scRNA / GEX / VDJ (E-MTAB-11278)
Organoid (E-MTAB-11267)
Visium (E-MTAB-11265)
ATAC-seq (E-MTAB-11266)
fetal-lung.cellgeni.sanger.ac.uk
genome.ucsc.edu
github.com
CELLxGENE
4,122 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
insitubiology.org
GSE197353
figshare.com
figshare.com
figshare.com
CELLxGENE
4,112 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Sncg gabaergic interneuron
Sncg gabaergic interneuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Sncg gabaergic interneuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Allen Brain Map
Reference middle temporal gyrus taxonomy
Allen Brain Map Patch-seq
assets.nemoarchive.org
github.com
CELLxGENE
4,101 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
+3
Oligodendrocyte precursor cell
Medulla oblongata
+7
Medulla oblongata
13th week post-fertilization stage
+4
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Oligodendrocyte
Committed oligodendrocyte precursor
Schwann cell
Tissue
Medulla oblongata
Hindbrain
Telencephalon
Midbrain
Cerebellum
Brain
Diencephalon
Pons
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
EGAS00001007472
Github
CELLxGENE
4,097 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
L5 extratelencephalic projecting glutamatergic cortical neuron
L5 extratelencephalic projecting glutamatergic cortical neuron
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
69-year-old stage
+20
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
L5 extratelencephalic projecting glutamatergic cortical neuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
69-year-old stage
75-year-old stage
42-year-old stage
89-year-old stage
87-year-old stage
85-year-old stage
88-year-old stage
68-year-old stage
29-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
80-year-old stage
72-year-old stage
81-year-old stage
80 year-old and over stage
77-year-old stage
86-year-old stage
70-year-old stage
78-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
UW Alzheimer's Disease Research Center
Adult Changes in Thought Study
UW BioRepository and Integrated Neuropathology
SEA-AD Homepage
AD Knowledge Portal
DOWNLOAD OFFICIAL DATASET
CELLxGENE
4,047 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+5
Endothelial cell
Thymus
Thymus
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell
Thymocyte
Macrophage
Dn4 thymocyte
Epithelial cell of thymus
Fibroblast
Tissue
Thymus
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
GSE132042
Processed files
Tabula Muris Senis
SmartSeq2 for HTP Generation of FACS Sorted Single Cell Libraries V.1
github.com
CELLxGENE
4,016 cells
•
Maatz et al., 2025
The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination
Explore
h5ad
Homo sapiens
Homo sapiens
Central memory cd4-positive, alpha-beta t cell
+12
Central memory cd4-positive, alpha-beta t cell
Apex of heart
+1
Apex of heart
21-year-old stage
+22
21-year-old stage
Myocarditis
+1
Myocarditis
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Central memory cd4-positive, alpha-beta t cell
Cycling t cell
Natural killer cell
Cytotoxic t cell
Mature nk t cell
Effector memory cd4-positive, alpha-beta t cell
Lymphocyte
T-helper 17 cell
Regulatory t cell
Effector t cell
Plasma cell
B cell
Effector memory cd8-positive, alpha-beta t cell
Tissue
Apex of heart
Heart left ventricle
Developmental stage
21-year-old stage
26-year-old stage
Sixth decade stage
61-year-old stage
52-year-old stage
30-year-old stage
29-year-old stage
38-year-old stage
Fifth decade stage
55-year-old stage
28-year-old stage
Third decade stage
49-year-old stage
24-year-old stage
Seventh decade stage
25-year-old stage
32-year-old stage
64-year-old stage
70-year-old stage
31-year-old stage
19-year-old stage
Eighth decade stage
27-year-old stage
Disease
Myocarditis
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
EGAS50000000769
PRJEB39602
EGAD00001009292
Reichart et al. (2022) Science
Litviňuková et al. (2020) Nature
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