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Technology
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Cell
934
Nucleus
679
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
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Most cells
Fewest cells
2515
datasets
CELLxGENE
29,769 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Podocyte
+13
Podocyte
Cortex of kidney
Cortex of kidney
56-year-old stage
56-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney granular cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Macula densa epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
56-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
CELLxGENE
29,674 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+22
T cell
Brodmann (1909) area 19
Brodmann (1909) area 19
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Cerebellar granule cell
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Microglial cell
Pericyte
Cerebral cortex neuron
Near-projecting glutamatergic cortical neuron
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Astrocyte
Fibroblast
Tissue
Brodmann (1909) area 19
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
data.nemoarchive.org
github (analysis and figures)
github (auto-annotations)
CELLxGENE
29,523 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
+2
Glutamatergic neuron
Medulla oblongata
+7
Medulla oblongata
13th week post-fertilization stage
+4
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glutamatergic neuron
Neuroblast (sensu nematoda and protostomia)
Neural progenitor cell
Tissue
Medulla oblongata
Hindbrain
Telencephalon
Midbrain
Cerebellum
Brain
Diencephalon
Pons
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
EGAS00001007472
Github
CELLxGENE
29,522 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+22
T cell
Inferior temporal gyrus
Inferior temporal gyrus
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Microglial cell
B cell
Pericyte
Cerebral cortex neuron
Near-projecting glutamatergic cortical neuron
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Astrocyte
Fibroblast
Tissue
Inferior temporal gyrus
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
data.nemoarchive.org
github (analysis and figures)
github (auto-annotations)
CELLxGENE
29,505 cells
•
Madissoon et al., 2022
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Explore
h5ad
Homo sapiens
Homo sapiens
Club cell
+11
Club cell
Bronchus
+4
Bronchus
66-year-old stage
+8
66-year-old stage
Normal
Normal
Female
+1
Female
10x 5' transcription profiling
+2
10x 5' transcription profiling
Nucleus
+1
Nucleus
Organism
Homo sapiens
Cell type
Club cell
Airway submucosal gland duct basal cell
Ciliated cell
Lung secretory cell
Neuroendocrine cell
Basal cell
Epithelial cell
Myoepithelial cell
Goblet cell
Deuterosomal cell
Serous secreting cell of bronchus submucosal gland
Respiratory tract suprabasal cell
Tissue
Bronchus
Lung
Trachea
Upper lobe of left lung
Lower lobe of left lung
Developmental stage
66-year-old stage
75-year-old stage
Sixth decade stage
29-year-old stage
35-year-old stage
Seventh decade stage
58-year-old stage
59-year-old stage
64-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' transcription profiling
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Cell
Related Links
PRJEB52292
explore.data.humancellatlas.org
E-MTAB-11640
S-BIAD570
5locationslung.cellgeni.sanger.ac.uk
CELLxGENE
29,498 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Intestine goblet cell
+6
Intestine goblet cell
Duodenum
+3
Duodenum
Carnegie stage 19
+10
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v2
+2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Intestine goblet cell
Best4+ enterocyte
Epithelial cell
Enteroendocrine cell
Intestinal crypt stem cell
Enterocyte
Progenitor cell
Tissue
Duodenum
Small intestine
Ileum
Jejunum
Developmental stage
Carnegie stage 19
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Embryonic stage
Carnegie stage 17
Carnegie stage 22
Carnegie stage 16
Carnegie stage 18
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Teichmann Lab
E-MTAB-14050
CELLxGENE
29,478 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
+18
Neutrophil
Mucosa of lip
+1
Mucosa of lip
65-year-old stage
+7
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Blood vessel endothelial cell
Natural killer cell
Endothelial cell of lymphatic vessel
Mast cell
Cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Schwann cell
Melanocyte
Myoepithelial cell
Macrophage
Mural cell
Keratinocyte
Acinar cell of salivary gland
Plasma cell
Salivary gland glandular cell
Langerhans cell
Fibroblast
Dendritic cell
Tissue
Mucosa of lip
Buccal mucosa
Developmental stage
65-year-old stage
61-year-old stage
39-year-old stage
56-year-old stage
28-year-old stage
24-year-old stage
33-year-old stage
22-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
github.com
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
Podocyte
+13
Podocyte
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
Podocyte
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney granular cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Macula densa epithelial 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
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
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
Mature cd4 single-positive thymocyte
+5
Mature cd4 single-positive thymocyte
Thymus
Thymus
24-day-old stage
+5
24-day-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Mature cd4 single-positive thymocyte
Double-positive, alpha-beta thymocyte
Leukocyte
Mature cd8 single-positive thymocyte
Cd8-positive, alpha-beta thymocyte
Cd4-positive, alpha-beta thymocyte
Tissue
Thymus
Developmental stage
24-day-old stage
5-week-old stage
4-week-old stage
7-week-old stage
6-week-old stage
10-week-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE186078
github.com
zenodo.org
s133.cs.berkeley.edu
s133.cs.berkeley.edu
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
69-year-old stage
+20
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Corticothalamic-projecting glutamatergic cortical neuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
69-year-old stage
75-year-old stage
42-year-old stage
89-year-old stage
87-year-old stage
85-year-old stage
88-year-old stage
68-year-old stage
29-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
80-year-old stage
72-year-old stage
81-year-old stage
80 year-old and over stage
77-year-old stage
86-year-old stage
70-year-old stage
78-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
UW Alzheimer's Disease Research Center
Adult Changes in Thought Study
UW BioRepository and Integrated Neuropathology
SEA-AD Homepage
AD Knowledge Portal
DOWNLOAD OFFICIAL DATASET
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
Photoreceptor cell r7
+5
Photoreceptor cell r7
Compound eye
Compound eye
Fully formed stage
Fully formed stage
Normal
Normal
Male
+1
Male
10x genomics v3
10x genomics v3
Organism
Drosophila melanogaster
Cell type
Photoreceptor cell r7
Photoreceptor cell r8
Compound eye cone cell
Eye photoreceptor cell
Interommatidial cell
Primary pigment cell
Tissue
Compound eye
Developmental stage
Fully formed stage
Disease
Normal
Sex
Male
Female
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
34-year-old stage
+8
34-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
34-year-old stage
53-year-old stage
48-year-old stage
29-year-old stage
28-year-old stage
24-year-old stage
Adult stage
33-year-old stage
41-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Zenodo code
GSE281356
HCA
1
2
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84
85
86
87
88
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