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Organism
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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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Suspension Type
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Cell
896
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
Single Cell Portal
13,805 cells
Explore
Oryctolagus cuniculus
Oryctolagus cuniculus
Intestinal crypt stem cell of large intestine
+5
Intestinal crypt stem cell of large intestine
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Oryctolagus cuniculus
Cell type
Intestinal crypt stem cell of large intestine
Best4+ enterocyte
Enteroendocrine cell
Transit amplifying cell
Large intestine goblet cell
Enterocyte of epithelium of large intestine
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
ASAP
13,788 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
+6
Neuron
Male reproductive gland
Male reproductive gland
Day 2 of adulthood
Day 2 of adulthood
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Neuron
Hemocyte
Spermatid
Muscle cell
Male accessory gland secondary cell
Spermatocyte
Male accessory gland main cell
Tissue
Male reproductive gland
Developmental stage
Day 2 of adulthood
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
Single Cell Portal
13,787 cells
Explore
Mus musculus
Mus musculus
Astrocyte
Astrocyte
Normal
Normal
Mixed sex
Mixed sex
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Mixed sex
Technology
10x 3' v2
Suspension type
CELLxGENE
13,782 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
+15
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
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
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
13,780 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
Endothelial cell
+8
Endothelial cell
Renal medulla
Renal medulla
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Tissue
Renal medulla
Developmental stage
64-year-old stage
Disease
Normal
Sex
Female
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
ASAP
13,774 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Visceral muscle cell
+1
Visceral muscle cell
Malpighian tubule
Malpighian tubule
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Visceral muscle cell
Adult renal stem cell
Tissue
Malpighian tubule
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
13,691 cells
•
Kamath et al., 2022
Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte precursor cell
Oligodendrocyte precursor cell
Substantia nigra pars compacta
Substantia nigra pars compacta
75-year-old stage
+12
75-year-old stage
Parkinson disease
+2
Parkinson disease
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte precursor cell
Tissue
Substantia nigra pars compacta
Developmental stage
75-year-old stage
91-year-old stage
89-year-old stage
92-year-old stage
82-year-old stage
90-year-old stage
74-year-old stage
49-year-old stage
70-year-old stage
78-year-old stage
76-year-old stage
79-year-old stage
83-year-old stage
Disease
Parkinson disease
Normal
Lewy body dementia
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
macoskolab.com
GEO series:GSE178265
BroadInstitute Single-Cell Portal:SCP1768
HumanCellAtlas:c412be53-cf95-47c7-980c-c0a0caa2d3a0
CELLxGENE
13,687 cells
•
Maksimovic et al., 2025
Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+9
Neutrophil
Lung
Lung
2-year-old stage
+9
2-year-old stage
Cystic fibrosis
+1
Cystic fibrosis
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Mast cell
Epithelial cell
Plasmacytoid dendritic cell
Plasma cell
Ciliated epithelial cell
B cell
Lung migratory dendritic cell
Monocyte
Conventional dendritic cell
Tissue
Lung
Developmental stage
2-year-old stage
8-year-old stage
6-month-old stage
10-month-old stage
3-year-old stage
1-year-old stage
11-month-old stage
5-year-old stage
6-year-old stage
4-year-old stage
Disease
Cystic fibrosis
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
protocols.io:processing-of-pediatric-bronchoalveolar-lavage-sam-6qpvr8ox2lmk/v1
CELLxGENE
13,635 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Periportal region hepatocyte
+5
Periportal region hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Late adult stage
+2
Late adult stage
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Periportal region hepatocyte
Hepatocyte
Centrilobular region hepatocyte
Midzonal region hepatocyte
Erythroid lineage cell
Erythroblast
Tissue
Caudate lobe of liver
Developmental stage
Late adult stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE243977
CELLxGENE
13,623 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
+25
Midbrain-derived inhibitory neuron
Nucleus of medulla oblongata
Nucleus of medulla oblongata
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
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Cerebellar granule cell
Lamp5 lhx6 neuron
Medial ganglionic eminence derived interneuron
Cerebellar inhibitory gabaergic interneuron
Ependymal cell
Microglial cell
Choroid plexus epithelial cell
Bergmann glial cell
Pericyte
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Purkinje cell
Vascular associated smooth muscle cell
Astrocyte
Unipolar brush cell
Fibroblast
Tissue
Nucleus of medulla oblongata
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
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
13,607 cells
•
Yan et al., 2020
Cell Atlas of The Human Fovea and Peripheral Retina
Explore
h5ad
Homo sapiens
Homo sapiens
Gabaergic amacrine cell
+1
Gabaergic amacrine cell
Peripheral region of retina
+1
Peripheral region of retina
69-year-old stage
+6
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Gabaergic amacrine cell
Glycinergic amacrine cell
Tissue
Peripheral region of retina
Fovea centralis
Developmental stage
69-year-old stage
65-year-old stage
53-year-old stage
74-year-old stage
64-year-old stage
60-year-old stage
78-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE148077
HumanCellAtlas:30dc3964-1135-4b56-b393-ce2dcbc6e379
BroadInstitute Single-Cell Portal:SCP839/cell-atlas-of-the-human-fovea-and-peripheral-retina
CELLxGENE
13,544 cells
•
Fink et al., 2022
Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
Explore
h5ad
Homo sapiens
Homo sapiens
Umbrella cell of urothelium
+2
Umbrella cell of urothelium
Ureter
Ureter
69-year-old stage
+8
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Umbrella cell of urothelium
Basal cell of urothelium
Intermediate cell of urothelium
Tissue
Ureter
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
85-year-old stage
68-year-old stage
82-year-old stage
81-year-old stage
74-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE184111
GEO series:GSE184112
UCSC Cell Browser:adult-ureter
Zenodo record:6762182
Github:2019surbhi/tinglab_ureter_analysis
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