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Disease
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Technology
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Cell
893
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
1,635 cells
•
Orozco et al., 2020
Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal pigment epithelial cell
Retinal pigment epithelial cell
Retina
Retina
77-year-old stage
+3
77-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Retinal pigment epithelial cell
Tissue
Retina
Developmental stage
77-year-old stage
79-year-old stage
65-year-old stage
70-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE135133
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
CELLxGENE
1,621 cells
•
Pan et al., 2024
Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profiling: a case study
Explore
h5ad
Homo sapiens
Homo sapiens
Microglial cell
Microglial cell
White matter of parietal lobe
+4
White matter of parietal lobe
68-year-old stage
+7
68-year-old stage
Alzheimer disease
+2
Alzheimer disease
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Microglial cell
Tissue
White matter of parietal lobe
Prefrontal cortex
White matter of frontal lobe
White matter of occipital lobe
White matter of temporal lobe
Developmental stage
68-year-old stage
82-year-old stage
83-year-old stage
76-year-old stage
72-year-old stage
81-year-old stage
53-year-old stage
70-year-old stage
Disease
Alzheimer disease
Leukoencephalopathy, diffuse hereditary, with spheroids 1
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE267301
CELLxGENE
1,562 cells
•
Anderson-Crannage et al., 2023
Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin
Explore
h5ad
Mus musculus
Mus musculus
Innate lymphoid cell
+3
Innate lymphoid cell
Autopod skin
Autopod skin
2-week-old stage
2-week-old stage
Epidermolysis bullosa
+1
Epidermolysis bullosa
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Innate lymphoid cell
Neutrophil
Professional antigen presenting cell
Mast cell
Tissue
Autopod skin
Developmental stage
2-week-old stage
Disease
Epidermolysis bullosa
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE222250
CELLxGENE
1,560 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Large intestine goblet cell
+8
Large intestine goblet cell
Colon
Colon
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Microcebus murinus
Cell type
Large intestine goblet cell
Intestinal enteroendocrine cell
Epithelial cell of large intestine
Enterocyte of epithelium of large intestine
Neutrophil
Cd8-positive, alpha-beta t cell
Fibroblast
Myeloid cell
Mesothelial cell
Tissue
Colon
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Smart-seq2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
app.globus.org
UCSC Cell Browser:tabula-microcebus
CELLxGENE
1,496 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Sst gabaergic interneuron
Sst gabaergic interneuron
Middle temporal gyrus
Middle temporal gyrus
43-year-old stage
+23
43-year-old stage
Dementia
+1
Dementia
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Sst gabaergic interneuron
Tissue
Middle temporal gyrus
Developmental stage
43-year-old stage
68-year-old stage
88-year-old stage
86-year-old stage
82-year-old stage
83-year-old stage
60-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
Adult stage
89-year-old stage
78-year-old stage
72-year-old stage
80 year-old and over stage
81-year-old stage
87-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
50-year-old stage
29-year-old stage
69-year-old stage
70-year-old stage
Disease
Dementia
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
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
Single Cell Portal
1,486 cells
Explore
Mus musculus
Mus musculus
Obsolete excitatory neuron
+3
Obsolete excitatory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete excitatory neuron
Oligodendrocyte precursor cell
Obsolete inhibitory neuron
Astrocyte of the cerebellum
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD704) (section 107)
CELLxGENE
1,465 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Caudal ganglionic eminence derived interneuron
Caudal ganglionic eminence derived 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
Caudal ganglionic eminence derived 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
1,417 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
Hepatic stellate cell
+2
Hepatic stellate cell
Caudate lobe of liver
Caudate lobe of liver
Young adult stage
+2
Young adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Hepatic stellate cell
Vascular associated smooth muscle cell
Vein endothelial cell
Tissue
Caudate lobe of liver
Developmental stage
Young adult stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
CELLxGENE
1,387 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
Pancreatic d cell
+3
Pancreatic d cell
Endocrine pancreas
Endocrine pancreas
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Pancreatic d cell
Pancreatic endocrine cell
Type b pancreatic cell
Pancreatic a cell
Tissue
Endocrine pancreas
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
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
1,378 cells
•
Orozco et al., 2020
Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
S cone cell
+1
S cone cell
Retina
Retina
77-year-old stage
+3
77-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
S cone cell
Retinal cone cell
Tissue
Retina
Developmental stage
77-year-old stage
79-year-old stage
65-year-old stage
70-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE135133
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
CELLxGENE
1,374 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
Hepatic stellate cell
+2
Hepatic stellate cell
Caudate lobe of liver
Caudate lobe of liver
Young adult stage
+1
Young adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Hepatic stellate cell
Vascular associated smooth muscle cell
Fibroblast
Tissue
Caudate lobe of liver
Developmental stage
Young adult stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Nucleus
Related Links
Github:tallulandrews/Liver_sc_sn_paper_scripts
GEO series:GSE185477
protocols.io:human-liver-caudate-lobe-dissociation-for-scrna-se-q26g77j1gwz1/v2
macparlandlab.shinyapps.io
HumanCellAtlas:8a666b76-daaf-4b1f-9414-e4807a1d1e8b
ASAP
1,349 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Adult neuron
+5
Adult neuron
Fat body
Fat body
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Organism
Drosophila melanogaster
Cell type
Adult neuron
Muscle cell
Epithelial cell
Hemocyte
Sensory neuron
Adult oenocyte
Tissue
Fat body
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
1
2
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