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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
CELLxGENE
14,424 cells
•
Sarieva et al., 2024
Comparing the impact of sample multiplexing approaches for single-cell RNA-sequencing on downstream analysis using cerebellar organoids
Explore
h5ad
Homo sapiens
Homo sapiens
Cerebellar neuron
+3
Cerebellar neuron
Cerebellum
Cerebellum
Fetal stage
Fetal stage
Normal
Normal
Female
+1
Female
Parse evercode whole transcriptome v2
+1
Parse evercode whole transcriptome v2
Cell
Cell
Organism
Homo sapiens
Cell type
Cerebellar neuron
Progenitor cell
Cerebellar granule cell precursor
Purkinje cell
Tissue
Cerebellum
Developmental stage
Fetal stage
Disease
Normal
Sex
Female
Male
Technology
Parse evercode whole transcriptome v2
10x 3' v3
Suspension type
Cell
CELLxGENE
14,411 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Cerebellar inhibitory gabaergic interneuron
Cerebellar inhibitory gabaergic interneuron
Pontine reticular formation
+29
Pontine reticular formation
42-year-old stage
+3
42-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cerebellar inhibitory gabaergic interneuron
Tissue
Pontine reticular formation
Medial dorsal nucleus of thalamus
Parabrachial nucleus
Nucleus of medulla oblongata
Red nucleus
Pontine tegmentum
Pontine nuclear group
Globus pallidus
Midbrain nucleus
Septal nuclear complex
Cerebellar nuclear complex
Extrastriate cortex
Epithalamus
Dorsal tegmental nucleus
Midbrain tectum
Inferior olivary complex
Substantia nigra
Cerebrocerebellum
Gray matter of midbrain
Substantia innominata
Hypothalamus
Primary motor cortex
Medial zone of hypothalamus
Posterior parahippocampal gyrus
Cerebellar vermis
Spinal cord
Mammillary body
Bed nucleus of stria terminalis
Lateral geniculate body
Pretectal region
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
60-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
ASAP
14,410 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Hemocyte
+2
Hemocyte
Oenocyte
Oenocyte
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Hemocyte
Adult alary muscle cell
Muscle cell
Tissue
Oenocyte
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
14,352 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+21
T cell
Brodmann (1909) area 14
Brodmann (1909) area 14
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Hippocampal ca1-3 neuron
Lamp5 lhx6 neuron
Eccentric medium spiny 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 14
Developmental stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
14,349 cells
•
Isola et al., 2024
A single-cell atlas of the aging mouse ovary
Explore
h5ad
Mus musculus
Mus musculus
T cell
+9
T cell
Ovary
Ovary
3-month-old stage
+1
3-month-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Phagocyte
Granulosa cell
Stromal cell
Endothelial cell
Luteal cell
Epithelial cell
Oocyte
B cell
Theca cell
Tissue
Ovary
Developmental stage
3-month-old stage
9-month-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:StoutLab/OvarianAgingAtlas
omrf.shinyapps.io
GEO series:GSE232309
CELLxGENE
14,344 cells
•
Yu et al., 2025
Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
Explore
h5ad
Homo sapiens
Homo sapiens
Macrophage
Macrophage
Neck
+6
Neck
13-year-old stage
+13
13-year-old stage
Neuroblastoma
Neuroblastoma
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Macrophage
Tissue
Neck
Liver
Abdomen
Chest
Adrenal gland
Lymph node
Cervical lymph node
Developmental stage
13-year-old stage
2-year-old stage
12-year-old stage
15-month-old stage
6-month-old stage
21-month-old stage
20-month-old stage
3-year-old stage
16-month-old stage
18-month-old stage
5-year-old stage
12-month-old stage
7-year-old stage
4-year-old stage
Disease
Neuroblastoma
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
Zenodo record:14261274
CELLxGENE
14,285 cells
•
Ulrich et al., 2021
Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
Explore
h5ad
Homo sapiens
Homo sapiens
Secretory cell
Secretory cell
Ampulla of fallopian tube
+3
Ampulla of fallopian tube
52-year-old stage
+3
52-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Secretory cell
Tissue
Ampulla of fallopian tube
Fimbria of fallopian tube
Fallopian tube
Isthmus of fallopian tube
Developmental stage
52-year-old stage
30-year-old stage
46-year-old stage
31-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE178101
HumanCellAtlas:21ea8ddb-525f-4f1f-a820-31f0360399a2
CELLxGENE
14,226 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+26
Midbrain-derived inhibitory neuron
Medial geniculate body
Medial geniculate body
42-year-old stage
+1
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Dentate gyrus granule cell
Cerebellar granule cell
Hippocampal ca1-3 neuron
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
Thalamic excitatory neuron
Pericyte
Neuron
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Sst chodl gabaergic interneuron
Astrocyte
Unipolar brush cell
Fibroblast
Mammillary body neuron
Tissue
Medial geniculate body
Developmental 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
14,213 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
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
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
DOI:10.5281/zenodo.14001210
HumanCellAtlas:df8eb7ce-3707-46af-b823-e081a562e954
GEO series:GSE281356
ASAP
14,197 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Hemocyte
+3
Hemocyte
Leg
Leg
Day 5 of adulthood
+1
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Hemocyte
Epithelial cell
Muscle cell
Mechanosensory neuron
Tissue
Leg
Developmental stage
Day 5 of adulthood
Day 2 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
14,186 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
+16
Podocyte
Renal medulla
Renal medulla
75-year-old stage
75-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Parietal epithelial cell
Endothelial cell
Kidney loop of henle thin descending limb epithelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule epithelial cell
Urothelial cell
Kidney loop of henle thick ascending limb epithelial cell
Kidney loop of henle epithelial cell
Mesangial cell
Pericyte
Kidney proximal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
75-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
grekalab.org
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
GEO series:GSE190094
CELLxGENE
14,177 cells
•
Apostolov et al., 2024
Profiling of epithelial functional states and fibroblast phenotypes in hormone therapy-naïve localised prostate cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+3
Endothelial cell of lymphatic vessel
Prostate gland
Prostate gland
69-year-old stage
+14
69-year-old stage
Prostatic acinar adenocarcinoma
Prostatic acinar adenocarcinoma
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Endothelial cell
Endothelial cell of coronary artery
Vein endothelial cell
Tissue
Prostate gland
Developmental stage
69-year-old stage
75-year-old stage
71-year-old stage
61-year-old stage
54-year-old stage
68-year-old stage
72-year-old stage
59-year-old stage
64-year-old stage
45-year-old stage
62-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
63-year-old stage
Disease
Prostatic acinar adenocarcinoma
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE145843
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