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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
5,785 cells
•
Chen et al., 2025
Determinants of sensitivity to HER2-targeted antibody drug conjugates in urothelial cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Neoplastic cell
Neoplastic cell
Urinary bladder
Urinary bladder
Adult stage
Adult stage
Urinary bladder cancer
Urinary bladder cancer
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neoplastic cell
Tissue
Urinary bladder
Developmental stage
Adult stage
Disease
Urinary bladder cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
5,779 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
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
Single Cell Portal
5,770 cells
Explore
Mus musculus
Mus musculus
Neuron
Neuron
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
5,762 cells
•
Chen et al., 2025
Determinants of sensitivity to HER2-targeted antibody drug conjugates in urothelial cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Neoplastic cell
Neoplastic cell
Urinary bladder
Urinary bladder
Adult stage
Adult stage
Urinary bladder cancer
Urinary bladder cancer
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neoplastic cell
Tissue
Urinary bladder
Developmental stage
Adult stage
Disease
Urinary bladder cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Single Cell Portal
5,759 cells
Explore
Homo sapiens
Homo sapiens
Gamma-delta t cell
+5
Gamma-delta t cell
Triple-negative breast carcinoma
Triple-negative breast carcinoma
10x 3' v2
10x 3' v2
Organism
Homo sapiens
Cell type
Gamma-delta t cell
Cd8-positive, alpha-beta memory t cell
Regulatory t cell
Cd4-positive, alpha-beta t cell
Cd4-positive, alpha-beta memory t cell
Monocyte
Tissue
Developmental stage
Disease
Triple-negative breast carcinoma
Sex
Technology
10x 3' v2
Suspension type
Related Links
Source publication
CELLxGENE
5,754 cells
•
Nowicki-Osuch et al., 2023
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Duodenum
+5
Duodenum
69-year-old stage
+21
69-year-old stage
Barrett esophagus
+3
Barrett esophagus
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Duodenum
Submucosal esophageal gland
Body of stomach
Cardia of stomach
Esophagogastric junction
Lower esophagus
Developmental stage
69-year-old stage
34-year-old stage
42-year-old stage
43-year-old stage
53-year-old stage
68-year-old stage
48-year-old stage
29-year-old stage
56-year-old stage
55-year-old stage
51-year-old stage
57-year-old stage
74-year-old stage
58-year-old stage
67-year-old stage
77-year-old stage
45-year-old stage
62-year-old stage
41-year-old stage
63-year-old stage
83-year-old stage
27-year-old stage
Disease
Barrett esophagus
Normal
Gastric intestinal metaplasia
Gastritis
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001010074
Github:karolno/BE-GIM_Comparison
CELLxGENE
5,733 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
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
GEO series:GSE197353
figshare.com
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
CELLxGENE
5,729 cells
•
Govek et al., 2022
Combined single-cell RNA-seq profiling and enhancer editing reveals critical spatiotemporal controls over thalamic nuclei formation in the murine embryo
Explore
h5ad
Mus musculus
Mus musculus
Glioblast
+2
Glioblast
Diencephalon
Diencephalon
Theiler stage 26
Theiler stage 26
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Glioblast
Glutamatergic neuron
Gabaergic neuron
Tissue
Diencephalon
Developmental stage
Theiler stage 26
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
5,697 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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
Chen Lab
GEO series:GSE197353
CELLxGENE
5,696 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
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
CELLxGENE
5,683 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+1
Endothelial 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
Endothelial cell
Pericyte
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
Github:linnarsson-lab/fetal_brain_multiomics
EGA Study:EGAS00001007472
CELLxGENE
5,666 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Osteoblast
+6
Osteoblast
Hypochord
+7
Hypochord
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Osteoblast
Kolmer-agduhr neuron
Endothelial cell
Retinal pigment epithelial cell
Mesodermal cell
Hatching gland cell
Primordial germ cell
Tissue
Hypochord
Interrenal primordium
Hatching gland
Gonad primordium
Multicellular anatomical structure
Pigmented layer of retina
Spinal cord
Blood island
Developmental stage
Pharyngula:prim-15
Hatching:long-pec
Larval:protruding-mouth
Pharyngula:prim-25
Segmentation:26+ somites
Segmentation:14-19 somites
Hatching:pec-fin
Segmentation:20-25 somites
Pharyngula:high-pec
Pharyngula:prim-5
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
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