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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
7,274 cells
•
Jin et al., 2021
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses
Explore
h5ad
Homo sapiens
Homo sapiens
Platelet
Platelet
Blood
Blood
75-year-old stage
+31
75-year-old stage
Covid-19
+1
Covid-19
Female
+1
Female
Seq-well
+2
Seq-well
Cell
Cell
Organism
Homo sapiens
Cell type
Platelet
Tissue
Blood
Developmental stage
75-year-old stage
Sixth decade stage
53-year-old stage
61-year-old stage
54-year-old stage
68-year-old stage
48-year-old stage
39-year-old stage
29-year-old stage
38-year-old stage
Fifth decade stage
84-year-old stage
82-year-old stage
Third decade stage
80 year-old and over stage
49-year-old stage
Seventh decade stage
59-year-old stage
Adult stage
67-year-old stage
62-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
78-year-old stage
36-year-old stage
Fourth decade stage
63-year-old stage
Eighth decade stage
47-year-old stage
73-year-old stage
27-year-old stage
Disease
Covid-19
Normal
Sex
Female
Male
Technology
Seq-well
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
cincinnatichildrens.org
toppcell.cchmc.org
CELLxGENE
7,249 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+16
T cell
Brain
Brain
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
T cell
Neural stem cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Mature nk t cell
Cd8-positive, alpha-beta t cell
Brain pericyte
Ependymal cell
Macrophage
Microglial cell
Interneuron
Bergmann glial cell
Neuron
Neuroepithelial stem cell
Astrocyte
Medium spiny neuron
Tissue
Brain
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
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
7,244 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Neutrophil
+25
Neutrophil
Urinary bladder
Urinary bladder
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
Neutrophil
Bladder urothelial cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Plasmacytoid dendritic cell
Lymphocyte
Adipocyte
Macrophage
Innate lymphoid cell
Plasma cell
Cd4-positive, alpha-beta t cell
Vein endothelial cell
Mesothelial cell
B cell
Pericyte
Monocyte
Vascular associated smooth muscle cell
Myofibroblast cell
Basophil
Conventional dendritic cell
Fibroblast
Myelinating schwann cell
Dendritic cell
Tissue
Urinary bladder
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
UCSC Cell Browser:tabula-microcebus
app.globus.org
CELLxGENE
7,233 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
+14
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
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
7,176 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
+13
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
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
Single Cell Portal
7,175 cells
Explore
Mus musculus
Mus musculus
Ependymal cell
+1
Ependymal cell
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Ependymal cell
Obsolete excitatory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD736) (section 280)
Corresponding registered brain section (MD736) (section 281)
Corresponding registered brain section (MD736) (section 283)
CELLxGENE
7,165 cells
•
Serizay et al., 2025
Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis
Explore
h5ad
Mus musculus
Mus musculus
Microglial cell
+5
Microglial cell
Multiciliated ependymal cell
Multiciliated ependymal cell
Theiler stage 27
Theiler stage 27
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Microglial cell
Neural crest derived fibroblast
Deuterosomal cell
Neuroblast (sensu vertebrata)
Radial glial cell
Neuron associated cell
Tissue
Multiciliated ependymal cell
Developmental stage
Theiler stage 27
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
DOI:10.1016/j.celrep.2024.115117
GEO series:GSE201773
DOI:10.5281/zenodo.14105247
CELLxGENE
7,156 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Corticothalamic-projecting glutamatergic cortical neuron
Corticothalamic-projecting glutamatergic cortical neuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Corticothalamic-projecting glutamatergic cortical neuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
knowledge.brain-map.org
Allen Brain Map:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
CELLxGENE
7,155 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Perivascular cell
+2
Perivascular cell
Forebrain meninges
+2
Forebrain meninges
13th week post-fertilization stage
+8
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Perivascular cell
Smooth muscle cell
Pericyte
Tissue
Forebrain meninges
Brain meninx
Meninx
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
Carnegie stage 23
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 16
Carnegie stage 18
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
7,138 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
+14
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
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
Chen Lab
GEO series:GSE197353
CELLxGENE
7,097 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
+6
Neutrophil
Blood
Blood
66-year-old stage
66-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Mature nk t cell
Platelet
Myeloid cell
Plasma cell
B cell
Dendritic cell
Tissue
Blood
Developmental stage
66-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
CELLxGENE
7,092 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
+7
Glutamatergic neuron
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
Glutamatergic neuron
Serotonergic neuron
Dopaminergic neuron
Neuroblast (sensu vertebrata)
Glycinergic neuron
Neuron
Sensory neuron of dorsal root ganglion
Gabaergic neuron
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
EGA Study:EGAS00001007472
Github:linnarsson-lab/fetal_brain_multiomics
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