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Disease
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Technology
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Cell
896
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
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
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:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
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
Cardiac endothelial cell
+8
Cardiac endothelial cell
Embryoid body
Embryoid body
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Endothelial cell
Hematopoietic precursor cell
Kidney interstitial fibroblast
Myeloid lineage restricted progenitor cell
Epithelial cell
Pluripotent stem cell
Vein endothelial cell
Progenitor cell
Tissue
Embryoid body
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE274084
GEO series:GSE274082
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
Dorsolateral prefrontal cortex
+26
Dorsolateral prefrontal cortex
Juvenile stage
+1
Juvenile stage
Normal
Normal
Female
+1
Female
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Macaca mulatta
Cell type
Ependymal cell
Tissue
Dorsolateral prefrontal cortex
Brodmann (1909) area 19
Medial dorsal nucleus of thalamus
Primary visual cortex
Ventral lateral nucleus of thalamus
Inferior temporal gyrus
Medulla oblongata
Prefrontal cortex
Midbrain
Entorhinal cortex
Nucleus accumbens
Cerebrocerebellum
Primary somatosensory cortex
Primary auditory cortex
Primary motor cortex
Inferior parietal cortex
Head of caudate nucleus
Corpus callosum
Hippocampal formation
Perirhinal cortex
Pons
Cerebellar vermis
Anterior cingulate cortex
Superior temporal sulcus
Superior parietal cortex
Lateral geniculate body
Amygdala
Developmental stage
Juvenile stage
Prime adult 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:7925943
Zenodo record:7925925
Zenodo record:7925933
CELLxGENE
7,027 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+21
Neutrophil
Right cardiac atrium
Right cardiac atrium
Fifth decade stage
+1
Fifth decade stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neutrophil
Endocardial cell
Dendritic cell, human
T-helper 2 cell
Endothelial cell
Mature nk t cell
Mast cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Plasma cell
Vein endothelial cell
Cd14-positive monocyte
Mesothelial cell
B cell
Regular atrial cardiac myocyte
Monocyte
Fibroblast of cardiac tissue
Tissue
Right cardiac atrium
Developmental stage
Fifth decade stage
Seventh 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-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
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
Neutrophil
+8
Neutrophil
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
Neutrophil
Erythrocyte
Mature nk t cell
Mast cell
Platelet
Epithelial cell
Myeloid cell
Plasma cell
B 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 pp cell
+3
Pancreatic pp 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 pp cell
Pancreatic a cell
Pancreatic d cell
Type b pancreatic 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
Cardiac valve cell
+12
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
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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
Single Cell Portal
6,969 cells
•
Falquet et al., 2023
Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations
Explore
Homo sapiens
Homo sapiens
Innate lymphoid cell
Innate lymphoid cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Homo sapiens
Cell type
Innate lymphoid cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
6,947 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
Neutrophil
+18
Neutrophil
Lung
Lung
Carnegie stage 19
+7
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Dendritic cell, human
Platelet
Classical monocyte
Plasmacytoid dendritic cell
Early lymphoid progenitor
Macrophage
Promonocyte
Bone marrow cell
Hematopoietic stem cell
Common myeloid progenitor
Eosinophil
Megakaryocyte
Granulocyte monocyte progenitor cell
Promyelocyte
Megakaryocyte-erythroid progenitor cell
Basophil
Dendritic cell
Non-classical monocyte
Tissue
Lung
Developmental stage
Carnegie stage 19
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
Carnegie stage 16
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11265
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11266
CELLxGENE
6,931 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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
6,877 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+19
Midbrain-derived inhibitory neuron
Lateral posterior nucleus of thalamus
Lateral posterior nucleus of thalamus
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Microglial cell
Thalamic excitatory neuron
Pericyte
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Lateral posterior nucleus of thalamus
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
6,847 cells
•
Stewart et al., 2019
Spatiotemporal immune zonation of the human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+12
Neutrophil
Kidney
Kidney
13th week post-fertilization stage
+5
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Natural killer cell
Mast cell
Cd8-positive, alpha-beta t cell
Erythroid lineage cell
Plasmacytoid dendritic cell
Lymphocyte
Macrophage
Cd4-positive, alpha-beta t cell
Megakaryocyte
B cell
Monocyte
Conventional dendritic cell
Tissue
Kidney
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
16th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
kidneycellatlas.org
HumanCellAtlas:abe1a013-af7a-45ed-8c26-f3793c24a1f4
UCSC Cell Browser:kidney-atlas
Single Cell Expression Atlas Experiment:E-HCAD-10
UCSC Genome Browser:hgTrackUi?db=hg38&g=kidneyStewart&position=default
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