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Tissue
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Disease
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Technology
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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
ASAP
6,527 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Neuron
+13
Neuron
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
Neuron
Fat cell
Tracheolar cell
Glial cell
Somatic precursor cell
Male germline cell
Hemocyte
Epithelial cell
Muscle cell
Adult glial cell
Sensory neuron
Oenocyte
Neuron
Female germline 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
CELLxGENE
6,512 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
Cranial motor neuron
+2
Cranial motor neuron
Multicellular anatomical structure
+2
Multicellular anatomical structure
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Cranial motor neuron
Lateral motor column neuron
Motor neuron
Tissue
Multicellular anatomical structure
Spinal cord
Head
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
CELLxGENE
6,497 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Endocardial cell
+15
Endocardial cell
Apex of heart
Apex of heart
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
Endocardial cell
Endothelial cell of lymphatic vessel
Endothelial cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Macrophage
Cd16-positive, cd56-dim natural killer cell, human
Glial cell
Vein endothelial cell
B cell
Pericyte
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Apex of heart
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-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
Bgee
6,490 cells
•
Guo et al., 2018
The adult human testis transcriptional cell atlas
Explore
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Homo sapiens (h5ad)
Homo sapiens
Homo sapiens
Endothelial cell
+9
Endothelial cell
Testis
Testis
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Male
Male
10x genomics v2
10x genomics v2
Organism
Homo sapiens
Cell type
Endothelial cell
Primary spermatocyte
Sertoli cell
Obsolete male germ line stem cell (sensu vertebrata)
Macrophage
Peritubular myoid cell
Spermatid
Sperm
Leydig cell
Spermatogonium
Tissue
Testis
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v2
Suspension type
Related Links
SRA Project:SRP135999
CELLxGENE
6,465 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Mechanoreceptor cell
+6
Mechanoreceptor cell
Forebrain meninges
+2
Forebrain meninges
13th week post-fertilization stage
+8
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Mechanoreceptor cell
Schwann cell
Epithelial cell
Neural crest cell
Neuroblast (sensu vertebrata)
Radial glial cell
Schwann cell precursor
Tissue
Forebrain meninges
Brain meninx
Meninx
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
Carnegie stage 23
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 16
Carnegie stage 18
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
6,362 cells
•
Matuck et al., 2026
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+7
Neutrophil
Minor salivary gland
+2
Minor salivary gland
34-year-old stage
+11
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Macrophage
Innate lymphoid cell
Plasma cell
B cell
Dendritic cell
Tissue
Minor salivary gland
Submandibular gland
Parotid gland
Developmental stage
34-year-old stage
26-year-old stage
Sixth decade stage
53-year-old stage
48-year-old stage
39-year-old stage
56-year-old stage
28-year-old stage
24-year-old stage
62-year-old stage
Fourth decade stage
40-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:Loci-lab/Oral-Craniofacial-Atlas
CELLxGENE
6,339 cells
•
Jones et al., 2024
Cellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencing
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+3
Endothelial cell
Ovary
Ovary
31-year-old stage
31-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell
Stromal cell of ovary
Leukocyte
Pericyte
Tissue
Ovary
Developmental stage
31-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE260685
CELLxGENE
6,289 cells
•
Andrews et al., 2021
Single‐Cell, Single‐Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Blood vessel endothelial cell
+2
Blood vessel endothelial cell
Caudate lobe of liver
Caudate lobe of liver
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Blood vessel endothelial cell
Endothelial cell of periportal hepatic sinusoid
Endothelial cell of pericentral hepatic sinusoid
Tissue
Caudate lobe of liver
Developmental stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Nucleus
Related Links
Github:tallulandrews/Liver_sc_sn_paper_scripts
HumanCellAtlas:8a666b76-daaf-4b1f-9414-e4807a1d1e8b
macparlandlab.shinyapps.io
GEO series:GSE185477
protocols.io:human-liver-caudate-lobe-dissociation-for-scrna-se-q26g77j1gwz1/v2
CELLxGENE
6,288 cells
•
Yao et al., 2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
+5
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
Smart-seq v4
Smart-seq v4
Cell
Cell
Organism
Mus musculus
Cell type
Glutamatergic neuron
Endothelial cell
Smooth muscle cell
Leptomeningeal cell
Astrocyte
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq v4
Suspension type
Cell
Related Links
DOI:10.17504/protocols.io.pjvdkn6
NeMo archive:dat-ch1nqb7
DOI:10.17504/protocols.io.bcbrism6
CELLxGENE
6,235 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
T cell
+32
T cell
Small intestine
Small intestine
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Microcebus murinus
Cell type
T cell
Neutrophil
Natural killer cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Mature nk t cell
Interstitial cell of cajal
Cd8-positive, alpha-beta t cell
Epithelial cell of small intestine
Endothelial cell of artery
Capillary endothelial cell
Enterocyte of epithelium of small intestine
Smooth muscle cell
Intestinal tuft cell
Lymphocyte
Small intestine goblet cell
Macrophage
Innate lymphoid cell
Myeloid cell
Intestinal enteroendocrine cell
Plasma cell
Cd4-positive, alpha-beta t cell
Vein endothelial cell
Eosinophil
Mesothelial cell
B cell
Pericyte
Vascular associated smooth muscle cell
Basophil
Conventional dendritic cell
Fibroblast
Dendritic cell
M cell of gut
Tissue
Small intestine
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
UCSC Cell Browser:tabula-microcebus
app.globus.org
CELLxGENE
6,210 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Liver
Liver
44-year-old stage
44-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Blood vessel endothelial cell
Blood vessel smooth muscle cell
Macrophage
Plasma cell
Malignant cell
Fibroblast
Tissue
Liver
Developmental stage
44-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
6,201 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+8
Endothelial cell
Pancreas
Pancreas
20-month-old stage and over
+1
20-month-old stage and over
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell
Pancreatic acinar cell
Pancreatic pp cell
Leukocyte
Pancreatic a cell
Pancreatic d cell
Pancreatic stellate cell
Type b pancreatic cell
Pancreatic ductal cell
Tissue
Pancreas
Developmental stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
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