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893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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Most cells
Fewest cells
2339
datasets
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 Atlases:rnaseq/human-mtg-10x_sea-ad
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map:classes/multimodal-characterization
CELLxGENE
7,155 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Pericyte
+2
Pericyte
Forebrain meninges
+2
Forebrain meninges
Carnegie stage 21
+8
Carnegie stage 21
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Pericyte
Perivascular cell
Smooth muscle cell
Tissue
Forebrain meninges
Brain meninx
Meninx
Developmental stage
Carnegie stage 21
10th week post-fertilization stage
9th week post-fertilization stage
Carnegie stage 20
Carnegie stage 16
Carnegie stage 23
Carnegie stage 18
13th week post-fertilization stage
12th week post-fertilization stage
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
Notochordal cell
+14
Notochordal cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Notochordal cell
Spinal cord interneuron
Paraxial cell
Neurectodermal cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal 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:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
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
Dendritic cell
+6
Dendritic cell
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
Dendritic cell
B cell
Neutrophil
Platelet
Mature nk t cell
Plasma cell
Myeloid 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
Serotonergic neuron
+7
Serotonergic neuron
Cerebellum
+7
Cerebellum
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
Serotonergic neuron
Neuroblast (sensu vertebrata)
Neuron
Dopaminergic neuron
Gabaergic neuron
Sensory neuron of dorsal root ganglion
Glutamatergic neuron
Glycinergic neuron
Tissue
Cerebellum
Brain
Hindbrain
Midbrain
Pons
Telencephalon
Diencephalon
Medulla oblongata
Developmental stage
10th week post-fertilization stage
9th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/fetal_brain_multiomics
EGA Study:EGAS00001007472
CELLxGENE
7,088 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Notochordal cell
+13
Notochordal cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Notochordal cell
Spinal cord interneuron
Paraxial cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal 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
7,056 cells
•
Wellington et al., 2025
Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney interstitial fibroblast
+8
Kidney interstitial fibroblast
Embryoid body
Embryoid body
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Kidney interstitial fibroblast
Progenitor cell
Myeloid lineage restricted progenitor cell
Cardiac endothelial cell
Endothelial cell
Hematopoietic precursor cell
Vein endothelial cell
Epithelial cell
Pluripotent stem cell
Tissue
Embryoid body
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE274082
GEO series:GSE274084
Github:FredHutch/Wellington-et-al-2024
CELLxGENE
7,055 cells
•
Chiou et al., 2023
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
Explore
h5ad
Macaca mulatta
Macaca mulatta
Ependymal cell
Ependymal cell
Corpus callosum
+26
Corpus callosum
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Macaca mulatta
Cell type
Ependymal cell
Tissue
Corpus callosum
Hippocampal formation
Entorhinal cortex
Brodmann (1909) area 19
Midbrain
Pons
Head of caudate nucleus
Medial dorsal nucleus of thalamus
Anterior cingulate cortex
Primary visual cortex
Dorsolateral prefrontal cortex
Superior parietal cortex
Superior temporal sulcus
Primary auditory cortex
Primary motor cortex
Prefrontal cortex
Ventral lateral nucleus of thalamus
Nucleus accumbens
Primary somatosensory cortex
Cerebellar vermis
Amygdala
Medulla oblongata
Cerebrocerebellum
Inferior parietal cortex
Perirhinal cortex
Inferior temporal gyrus
Lateral geniculate body
Developmental stage
Prime adult stage
Juvenile stage
Disease
Normal
Sex
Female
Male
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
DOI:10.17504/protocols.io.9yih7ue
NeMo archive:dat-rtmm5q2
Zenodo record:7925933
Zenodo record:7925925
Zenodo record:7925943
CELLxGENE
7,027 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
+21
Regular atrial cardiac myocyte
Right cardiac atrium
Right cardiac atrium
Seventh decade stage
+1
Seventh decade stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Regular atrial cardiac myocyte
T-helper 2 cell
B cell
Endothelial cell of artery
Glial cell
Neutrophil
Monocyte
Mature nk t cell
Smooth muscle cell
Macrophage
Fibroblast of cardiac tissue
Adipocyte
Smooth muscle cell of the pulmonary artery
Endothelial cell
Cd14-positive monocyte
Dendritic cell, human
Endocardial cell
Vein endothelial cell
Plasma cell
Mast cell
Mesothelial cell
Cd16-positive, cd56-dim natural killer cell, human
Tissue
Right cardiac atrium
Developmental stage
Seventh decade stage
Fifth decade stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
7,025 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
B cell
+8
B cell
Respiratory airway
Respiratory airway
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
B cell
Neutrophil
Platelet
Mature nk t cell
Erythrocyte
Epithelial cell
Plasma cell
Mast cell
Myeloid cell
Tissue
Respiratory airway
Developmental stage
66-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
CELLxGENE
7,011 cells
•
Tritschler et al., 2022
A transcriptional cross species map of pancreatic islet cells
Explore
h5ad
Mus musculus
Mus musculus
Pancreatic d cell
+3
Pancreatic d cell
Islet of langerhans
Islet of langerhans
5-month-old stage
5-month-old stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Pancreatic d cell
Type b pancreatic cell
Pancreatic pp cell
Pancreatic a cell
Tissue
Islet of langerhans
Developmental stage
5-month-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE128565
GEO series:GSE198623
CELLxGENE
6,984 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Spinal cord interneuron
+12
Spinal cord interneuron
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Spinal cord interneuron
Paraxial cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal 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
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