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Cell Type
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Tissue
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Developmental Stage
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Disease
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Sex
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Technology
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Cell
893
Nucleus
659
Data Source
0
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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
8,425 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
Bgee
8,413 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Gallus gallus (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Gallus gallus (h5ad)
Gallus gallus
Gallus gallus
Sertoli cell
+5
Sertoli cell
Testis
Testis
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Male
Male
10x genomics v3
10x genomics v3
Organism
Gallus gallus
Cell type
Sertoli cell
Obsolete somatic cell
Late spermatid
Spermatocyte
Spermatogonium
Early spermatid
Tissue
Testis
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v3
Suspension type
Related Links
ebi.ac.uk
CELLxGENE
8,365 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Plasmacytoid dendritic cell
+21
Plasmacytoid dendritic cell
Liver
Liver
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Microcebus murinus
Cell type
Plasmacytoid dendritic cell
Natural killer cell
Dendritic cell
Erythroid lineage cell
Hepatocyte
Endothelial cell of hepatic sinusoid
B cell
Conventional dendritic cell
Neutrophil
Lymphocyte
Monocyte
Mature nk t cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Endothelial cell
Intrahepatic cholangiocyte
Hematopoietic precursor cell
Basophil
Fibroblast
Plasma cell
Mesothelial cell
Tissue
Liver
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Smart-seq2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
UCSC Cell Browser:tabula-microcebus
app.globus.org
CELLxGENE
8,362 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
Glutamatergic neuron
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
Glutamatergic neuron
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
8,345 cells
•
Stewart et al., 2019
Spatiotemporal immune zonation of the human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Neuron
+3
Neuron
Kidney
Kidney
10th week post-fertilization stage
+5
10th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Neuron
Myofibroblast cell
Mesenchymal stem cell
Fibroblast
Tissue
Kidney
Developmental stage
10th week post-fertilization stage
9th week post-fertilization stage
16th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
kidneycellatlas.org
UCSC Cell Browser:kidney-atlas
UCSC Genome Browser:hgTrackUi?db=hg38&g=kidneyStewart&position=default
Single Cell Expression Atlas Experiment:E-HCAD-10
HumanCellAtlas:abe1a013-af7a-45ed-8c26-f3793c24a1f4
CELLxGENE
8,311 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Large intestine goblet cell
+6
Large intestine goblet cell
Large intestine
Large intestine
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Large intestine goblet cell
Epithelial cell of large intestine
Enterocyte of epithelium of large intestine
Secretory cell
Tuft cell of large intestine
Enteroendocrine cell
Intestinal crypt stem cell
Tissue
Large intestine
Developmental stage
20-month-old stage and over
18-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
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
Single Cell Portal
8,308 cells
•
Ziegler et al., 2020
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Explore
Macaca mulatta
Macaca mulatta
Plasmacytoid dendritic cell
+24
Plasmacytoid dendritic cell
Disease
+1
Disease
Seq-well
Seq-well
Organism
Macaca mulatta
Cell type
Plasmacytoid dendritic cell
Pulmonary alveolar type 2 cell
Dendritic cell
Goblet cell
Tuft cell
T cell
Epithelial fate stem cell
Alveolar macrophage
Club cell
B cell
Non-classical monocyte
Enterocyte
Enteroendocrine cell
Enterocyte of epithelium proper of large intestine
Pre-natural killer cell
Basophil mast progenitor cell
Endothelial cell
Cd14-positive monocyte
Pulmonary alveolar type 1 cell
Ciliated epithelial cell
Epithelial cell
Fibroblast
Plasma cell
Mast cell
Eosinophil
Tissue
Developmental stage
Disease
Disease
Hiv infectious disease
Sex
Technology
Seq-well
Suspension type
Related Links
cellxgene.cziscience.com
cellxgene.cziscience.com
ASAP
8,304 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Male germline cell
+13
Male germline cell
Haltere
Haltere
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Male germline cell
Neuron
Tracheolar cell
Neuron
Adult glial cell
Muscle cell
Fat cell
Epithelial cell
Female germline cell
Hemocyte
Sensory neuron
Oenocyte
Somatic precursor cell
Glial cell
Tissue
Haltere
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
Single Cell Portal
8,268 cells
Explore
Mus musculus
Mus musculus
Pituitary gland cell
Pituitary gland cell
Normal
Normal
Mixed sex
Mixed sex
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Pituitary gland cell
Tissue
Developmental stage
Disease
Normal
Sex
Mixed sex
Technology
10x 3' v3
Suspension type
CELLxGENE
8,263 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Myoepithelial cell
+6
Myoepithelial cell
Parotid gland
+1
Parotid gland
34-year-old stage
+4
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Myoepithelial cell
Melanocyte
Salivary gland glandular cell
Basal cell
Ionocyte
Epithelial cell
Acinar cell of salivary gland
Tissue
Parotid gland
Labial gland
Developmental stage
34-year-old stage
68-year-old stage
24-year-old stage
28-year-old stage
26-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
8,242 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
CELLxGENE
8,213 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
L6b glutamatergic cortical neuron
L6b 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
L6b 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
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