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Disease
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Technology
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Cell
893
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
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
Gabaergic neuron
Glutamatergic 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
Notochordal cell
+15
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
Anterior visceral endoderm cell
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:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
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
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
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
Pericyte
+1
Pericyte
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
Pericyte
Endothelial cell
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
EGA Study:EGAS00001007472
Github:linnarsson-lab/fetal_brain_multiomics
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
Interrenal primordium
+7
Interrenal primordium
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Osteoblast
Retinal pigment epithelial cell
Kolmer-agduhr neuron
Hatching gland cell
Endothelial cell
Mesodermal cell
Primordial germ cell
Tissue
Interrenal primordium
Multicellular anatomical structure
Hatching gland
Pigmented layer of retina
Gonad primordium
Blood island
Hypochord
Spinal cord
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
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
CELLxGENE
5,625 cells
•
Xiang et al., 2020
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
Peripheral lymph node
Peripheral lymph node
Prime adult stage
Prime adult stage
Lymphadenitis
+1
Lymphadenitis
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell of lymphatic vessel
Tissue
Peripheral lymph node
Developmental stage
Prime adult stage
Disease
Lymphadenitis
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
med.stanford.edu
GEO series:GSE145121
igp.uu.se
GEO series:GSE143877
CELLxGENE
5,617 cells
•
Joseph et al., 2021
Single‐cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions
Explore
h5ad
Mus musculus
Mus musculus
Smooth muscle cell of prostate
+2
Smooth muscle cell of prostate
Prostate gland
+1
Prostate gland
2-month-old stage
2-month-old stage
Normal
Normal
Male
Male
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Smooth muscle cell of prostate
Fibroblast of connective tissue of prostate
Fibroblast
Tissue
Prostate gland
Urethra
Developmental stage
2-month-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
DOI:10.25548/17-DRBC
GEO series:GSE172357
GEO series:GSE173096
strandlab.net
CELLxGENE
5,613 cells
•
Alkaslasi et al., 2021
Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord
Explore
h5ad
Mus musculus
Mus musculus
Visceromotor neuron
Visceromotor neuron
Thoracic spinal cord
+2
Thoracic spinal cord
8-week-old stage
8-week-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Visceromotor neuron
Tissue
Thoracic spinal cord
Cervical spinal cord
Lumbar spinal cord
Developmental stage
8-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
CELLxGENE
5,608 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
+5
Dendritic cell
Blood
Blood
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
Dendritic cell
B cell
Platelet
Mature nk t cell
Plasma cell
Myeloid cell
Tissue
Blood
Developmental stage
74-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
5,572 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Mature microglial cell
Mature microglial cell
Entorhinal cortex
Entorhinal cortex
82-year-old stage
+7
82-year-old stage
Alzheimer disease
+1
Alzheimer disease
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mature microglial cell
Tissue
Entorhinal cortex
Developmental stage
82-year-old stage
60-year-old stage
77-year-old stage
72-year-old stage
80 year-old and over stage
87-year-old stage
50-year-old stage
71-year-old stage
Disease
Alzheimer disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
GEO series:GSE147528
kampmannlab.ucsf.edu
synapse.org:#!Synapse:syn21788402/wiki/601825
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
CELLxGENE
5,535 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
+15
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
Anterior visceral endoderm cell
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
5,500 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Mature astrocyte
Mature astrocyte
Entorhinal cortex
Entorhinal cortex
82-year-old stage
+7
82-year-old stage
Alzheimer disease
+1
Alzheimer disease
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mature astrocyte
Tissue
Entorhinal cortex
Developmental stage
82-year-old stage
60-year-old stage
77-year-old stage
72-year-old stage
80 year-old and over stage
87-year-old stage
50-year-old stage
71-year-old stage
Disease
Alzheimer disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
GEO series:GSE147528
kampmannlab.ucsf.edu
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
synapse.org:#!Synapse:syn21788402/wiki/601825
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