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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
7,999 cells
•
Reichart et al., 2022
Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac neuron
Cardiac neuron
Heart left ventricle
+3
Heart left ventricle
Fourth decade stage
+7
Fourth decade stage
Dilated cardiomyopathy
+3
Dilated cardiomyopathy
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cardiac neuron
Tissue
Heart left ventricle
Heart right ventricle
Interventricular septum
Apex of heart
Developmental stage
Fourth decade stage
Seventh decade stage
Postnatal stage
Fifth decade stage
Pediatric stage
Sixth decade stage
Eighth decade stage
Third decade stage
Disease
Dilated cardiomyopathy
Arrhythmogenic right ventricular cardiomyopathy
Normal
Non-compaction cardiomyopathy
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Nucleus
Related Links
Github:heiniglab/DCM_heart_cell_atlas
Zenodo record:6962685#.YuyuihxBzKE
EGA Study:EGAS00001006374
CELLxGENE
7,976 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Smooth muscle cell of trachea
+11
Smooth muscle cell of trachea
Trachea
Trachea
3-month-old stage
3-month-old stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Smooth muscle cell of trachea
Neuroendocrine cell
Mesenchymal cell
Macrophage
Endothelial cell
Mesenchymal stem cell
Granulocyte
Chondrocyte
Epithelial cell
Fibroblast
Blood cell
Basal epithelial cell of tracheobronchial tree
Tissue
Trachea
Developmental stage
3-month-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE132042
CZ BioHub Portal:tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CELLxGENE
7,846 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
7,805 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
60-year-old stage
+1
60-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
60-year-old stage
50-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
Github:AllenInstitute/BICCN_M1_Evo
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
CELLxGENE
7,803 cells
•
Stewart et al., 2019
Spatiotemporal immune zonation of the human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+11
Plasmacytoid dendritic cell
Cortex of kidney
+4
Cortex of kidney
49-year-old stage
+11
49-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Natural killer cell
Dendritic cell
Kidney resident macrophage
B cell
Non-classical monocyte
Neutrophil
Classical monocyte
Mature nk t cell
Cd4-positive, alpha-beta t cell
Cd8-positive, alpha-beta t cell
Mast cell
Tissue
Cortex of kidney
Renal medulla
Kidney
Kidney blood vessel
Renal pelvis
Developmental stage
49-year-old stage
64-year-old stage
4-year-old stage
63-year-old stage
72-year-old stage
67-year-old stage
2-year-old stage
12-year-old stage
44-year-old stage
19-month-old stage
53-year-old stage
70-year-old 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
UCSC Genome Browser:hgTrackUi?db=hg38&g=kidneyStewart&position=default
Single Cell Expression Atlas Experiment:E-HCAD-10
Single Cell Portal
7,787 cells
Explore
Mus musculus
Mus musculus
Oligodendrocyte
+5
Oligodendrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Oligodendrocyte
Obsolete excitatory neuron
Microglial cell
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Astrocyte of the cerebellum
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD702) (section 584)
Single Cell Portal
7,787 cells
Explore
Mus musculus
Mus musculus
Oligodendrocyte
+5
Oligodendrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Oligodendrocyte
Obsolete excitatory neuron
Microglial cell
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Astrocyte of the cerebellum
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD705) (section 107)
CELLxGENE
7,777 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
+4
Osteoblast
Cleithrum
+2
Cleithrum
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
Mesenchymal cell
Tendon cell
Chondrocyte
Mesodermal cell
Tissue
Cleithrum
Pectoral fin
Pectoral appendage bud
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
7,774 cells
•
Vinsland et al., 2025
Organotypic Timelapse recording with Transcriptomic Readout (OTTR) links cell behaviour to cell identity in human tissues
Explore
h5ad
Homo sapiens
Homo sapiens
Neuron associated cell
+9
Neuron associated cell
Telencephalon
Telencephalon
Carnegie stage 20
+1
Carnegie stage 20
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neuron associated cell
Microglial cell
Oligodendrocyte precursor cell
Forebrain neuroblast
Gabaergic neuron
Thalamic excitatory neuron
Fibroblast
Cajal-retzius cell
Glutamatergic neuron
Radial glial cell
Tissue
Telencephalon
Developmental stage
Carnegie stage 20
Carnegie stage 23
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/OTTR
CELLxGENE
7,750 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+8
Plasmacytoid dendritic cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Cd14-low, cd16-positive monocyte
Natural killer cell
Dendritic cell
B cell
Cd4-positive, alpha-beta t cell
Megakaryocyte
Cd14-positive monocyte
Cytotoxic t cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:danledinh/scRNAseq-repo
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
CELLxGENE
7,750 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+8
Plasmacytoid dendritic cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
Hive clx single-cell rnaseq solution
Hive clx single-cell rnaseq solution
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Cd14-low, cd16-positive monocyte
Natural killer cell
Dendritic cell
B cell
Cd4-positive, alpha-beta t cell
Megakaryocyte
Cd14-positive monocyte
Cytotoxic t cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
Hive clx single-cell rnaseq solution
Suspension type
Cell
Related Links
Github:danledinh/scRNAseq-repo
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
CELLxGENE
7,750 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+8
Plasmacytoid dendritic cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
Scalebio single cell rna sequencing
Scalebio single cell rna sequencing
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Cd14-low, cd16-positive monocyte
Natural killer cell
Dendritic cell
B cell
Cd4-positive, alpha-beta t cell
Megakaryocyte
Cd14-positive monocyte
Cytotoxic t cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
Scalebio single cell rna sequencing
Suspension type
Cell
Related Links
Github:danledinh/scRNAseq-repo
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
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