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Disease
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Technology
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Cell
890
Nucleus
655
Data Source
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Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
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Most cells
Fewest cells
2328
datasets
CELLxGENE
29,478 cells
•
Fernandes Matuck et al., 2024
The Immunoregulatory Architecture of the Adult Oral Cavity
Explore
h5ad
Homo sapiens
Homo sapiens
Myoepithelial cell
+18
Myoepithelial cell
Mucosa of lip
+1
Mucosa of lip
22-year-old stage
+7
22-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Myoepithelial cell
Schwann cell
Mural cell
Endothelial cell of lymphatic vessel
Macrophage
Mast cell
Cd4-positive helper t cell
Neutrophil
Acinar cell of salivary gland
Fibroblast
Blood vessel endothelial cell
Salivary gland glandular cell
Cd8-positive, alpha-beta t cell
Dendritic cell
Plasma cell
Keratinocyte
Natural killer cell
Melanocyte
Langerhans cell
Tissue
Mucosa of lip
Buccal mucosa
Developmental stage
22-year-old stage
33-year-old stage
65-year-old stage
28-year-old stage
56-year-old stage
61-year-old stage
24-year-old stage
39-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:Loci-lab/Oral-Craniofacial-Atlas
CELLxGENE
29,434 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Mus musculus
Mus musculus
Kidney loop of henle thick ascending limb epithelial cell
+13
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
6-month-old stage
6-month-old stage
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic kidney disease
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Macula densa epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-old stage
Disease
Autosomal dominant polycystic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
29,408 cells
•
Steier et al., 2023
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment
Explore
h5ad
Mus musculus
Mus musculus
Cd8-positive, alpha-beta thymocyte
+5
Cd8-positive, alpha-beta thymocyte
Thymus
Thymus
7-week-old stage
+5
7-week-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Cd8-positive, alpha-beta thymocyte
Double-positive, alpha-beta thymocyte
Leukocyte
Mature cd4 single-positive thymocyte
Cd4-positive, alpha-beta thymocyte
Mature cd8 single-positive thymocyte
Tissue
Thymus
Developmental stage
7-week-old stage
10-week-old stage
24-day-old stage
4-week-old stage
5-week-old stage
6-week-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Zenodo record:8102050
s133.cs.berkeley.edu
s133.cs.berkeley.edu
GEO series:GSE186078
Github:YosefLab/Thymus_CITE-seq
CELLxGENE
29,343 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Corticothalamic-projecting glutamatergic cortical neuron
Corticothalamic-projecting glutamatergic cortical neuron
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
80-year-old stage
+20
80-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Corticothalamic-projecting glutamatergic cortical neuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
80-year-old stage
85-year-old stage
82-year-old stage
70-year-old stage
77-year-old stage
50-year-old stage
86-year-old stage
80 year-old and over stage
89-year-old stage
75-year-old stage
78-year-old stage
68-year-old stage
42-year-old stage
72-year-old stage
88-year-old stage
84-year-old stage
69-year-old stage
29-year-old stage
87-year-old stage
81-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x 3' v3
10x multiome
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
Allen Brain Map:seattle-alzheimers-disease
AWS Open Data:allen-sea-ad-atlas
AD knowledge portal:syn26223298
Bgee
29,084 cells
•
Yeung et al., 2022
Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types
Explore
scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster (h5ad)
Drosophila melanogaster
Drosophila melanogaster
Primary pigment cell
+5
Primary pigment cell
Compound eye
Compound eye
Fully formed stage
Fully formed stage
Normal
Normal
Female
+1
Female
10x genomics v3
10x genomics v3
Organism
Drosophila melanogaster
Cell type
Primary pigment cell
Compound eye cone cell
Eye photoreceptor cell
Photoreceptor cell r7
Interommatidial cell
Photoreceptor cell r8
Tissue
Compound eye
Developmental stage
Fully formed stage
Disease
Normal
Sex
Female
Male
Technology
10x genomics v3
Suspension type
Related Links
SRA Project:SRP400422
CELLxGENE
29,078 cells
•
Lazarescu et al., 2025
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
Explore
h5ad
Homo sapiens
Homo sapiens
Adipocyte of omentum tissue
+1
Adipocyte of omentum tissue
Visceral fat
Visceral fat
48-year-old stage
+8
48-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Adipocyte of omentum tissue
Mesenchymal stem cell of adipose tissue
Tissue
Visceral fat
Developmental stage
48-year-old stage
33-year-old stage
Adult stage
28-year-old stage
34-year-old stage
53-year-old stage
24-year-old stage
29-year-old stage
41-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14001210
HumanCellAtlas:df8eb7ce-3707-46af-b823-e081a562e954
GEO series:GSE281356
CELLxGENE
29,041 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
Oligodendrocyte precursor cell
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
80-year-old stage
+20
80-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Tissue
Dorsolateral prefrontal cortex
Developmental stage
80-year-old stage
85-year-old stage
82-year-old stage
70-year-old stage
77-year-old stage
50-year-old stage
86-year-old stage
80 year-old and over stage
89-year-old stage
75-year-old stage
78-year-old stage
68-year-old stage
42-year-old stage
72-year-old stage
88-year-old stage
84-year-old stage
69-year-old stage
29-year-old stage
87-year-old stage
81-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x 3' v3
10x multiome
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
Allen Brain Map:seattle-alzheimers-disease
AWS Open Data:allen-sea-ad-atlas
AD knowledge portal:syn26223298
CELLxGENE
29,011 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Mus musculus
Mus musculus
Kidney loop of henle thick ascending limb epithelial cell
+13
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
13-week-old stage
13-week-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Macula densa epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
13-week-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
28,984 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+9
Astrocyte
Lateral amygdaloid nucleus
Lateral amygdaloid nucleus
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Fibroblast
Ependymal cell
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Lateral amygdaloid nucleus
Developmental stage
50-year-old stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
28,943 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Sst gabaergic interneuron
Sst gabaergic interneuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Sst gabaergic interneuron
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
Allen Brain Map:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
CELLxGENE
28,867 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Schwann cell
+8
Schwann cell
Limb muscle
Limb muscle
3-month-old stage
+3
3-month-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Schwann cell
Mesenchymal stem cell
Macrophage
Cell of skeletal muscle
Endothelial cell
Skeletal muscle satellite cell
B cell
T cell
Smooth muscle cell
Tissue
Limb muscle
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
4-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
GEO series:GSE132042
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
28,847 cells
•
Joseph et al., 2020
Urethral luminal epithelia are castration‐insensitive cells of the proximal prostate
Explore
h5ad
Homo sapiens
Homo sapiens
Luminal cell of prostate epithelium
+8
Luminal cell of prostate epithelium
Transition zone of prostate
+1
Transition zone of prostate
57-year-old stage
+4
57-year-old stage
Normal
+1
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Luminal cell of prostate epithelium
Prostate stromal cell
Leukocyte
Basal cell of prostate epithelium
Epithelial cell of urethra
Smooth muscle cell of prostate
Prostate gland microvascular endothelial cell
Secretory cell
Neuroendocrine cell
Tissue
Transition zone of prostate
Peripheral zone of prostate
Developmental stage
57-year-old stage
74-year-old stage
31-year-old stage
72-year-old stage
29-year-old stage
Disease
Normal
Benign prostatic hyperplasia
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
strandlab.net
GEO series:GSE145928
DOI:10.25548/16-WM8C
GEO series:GSE145929
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