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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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Cell
871
Nucleus
653
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,045
Single cell portal
176
Sort
Most cells
Fewest cells
2304
datasets
ASAP
100,527 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
Head
Head
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+2
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Hemocyte
Adult brain perineurial glial cell
Adult somatic muscle cell of head
Tissue
Head
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Mixed sex
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
100,307 cells
•
Garcia-Alonso et al., 2021
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+9
Fibroblast
Endometrium
Endometrium
26-year-old stage
+4
26-year-old stage
Normal
Normal
Female
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Myeloid cell
Epithelial cell
Uterine smooth muscle cell
Stromal cell of ovary
Endothelial cell of uterus
Glandular secretory epithelial cell
Supporting cell
Leukocyte
Ciliated cell
Tissue
Endometrium
Developmental stage
26-year-old stage
Third decade stage
29-year-old stage
Young adult stage
37-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-10287
ArrayExpress BioStudies:E-MTAB-9260
ArrayExpress BioStudies:E-MTAB-10283
EGA dataset:EGAD00001007909
HumanCellAtlas:2b38025d-a5ea-4c0f-b22e-367824bcaf4c
CELLxGENE
100,215 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Vip gabaergic interneuron
Vip gabaergic interneuron
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
78-year-old stage
+20
78-year-old stage
Dementia
+1
Dementia
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Vip gabaergic interneuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
78-year-old stage
80 year-old and over stage
72-year-old stage
83-year-old stage
85-year-old stage
81-year-old stage
82-year-old stage
42-year-old stage
86-year-old stage
70-year-old stage
75-year-old stage
50-year-old stage
89-year-old stage
68-year-old stage
29-year-old stage
77-year-old stage
69-year-old stage
88-year-old stage
87-year-old stage
80-year-old stage
84-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
AD knowledge portal:syn26223298
AWS Open Data:allen-sea-ad-atlas
Allen Brain Map:seattle-alzheimers-disease
CELLxGENE
100,064 cells
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmablast
+17
Plasmablast
Breast
Breast
54-year-old stage
+19
54-year-old stage
Invasive lobular breast carcinoma
+2
Invasive lobular breast carcinoma
Female
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmablast
Luminal epithelial cell of mammary gland
Myeloid cell
Memory b cell
Mammary gland epithelial cell
Pericyte
Cd8-positive, alpha-beta t cell
Endothelial cell of lymphatic vessel
Natural killer cell
Macrophage
Monocyte
Basal-myoepithelial cell of mammary gland
Mature nk t cell
Cd4-positive, alpha-beta t cell
T cell
Naive b cell
Fibroblast of breast
Endothelial cell
Tissue
Breast
Developmental stage
54-year-old stage
35-year-old stage
73-year-old stage
85-year-old stage
61-year-old stage
57-year-old stage
82-year-old stage
49-year-old stage
42-year-old stage
52-year-old stage
41-year-old stage
55-year-old stage
58-year-old stage
50-year-old stage
88-year-old stage
63-year-old stage
60-year-old stage
67-year-old stage
43-year-old stage
47-year-old stage
Disease
Invasive lobular breast carcinoma
Breast carcinoma
Invasive ductal breast carcinoma
Sex
Female
Technology
10x 3' v3
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
EGA Study:EGAS00001005173
Zenodo record:4739739
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
CELLxGENE
100,055 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 ganglion cell
+9
Retinal ganglion cell
Retina
Retina
70-year-old stage
+3
70-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Retinal ganglion cell
Retinal rod cell
Myeloid cell
Astrocyte
Amacrine cell
Retina horizontal cell
Retinal bipolar neuron
Retinal pigment epithelial cell
Retinal cone cell
Mueller cell
Tissue
Retina
Developmental stage
70-year-old stage
79-year-old stage
77-year-old stage
65-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
Single Cell Portal
99,684 cells
Explore
Homo sapiens
Homo sapiens
Mast cell
+11
Mast cell
Cardiomyopathy
+1
Cardiomyopathy
10x 3' v3
10x 3' v3
Organism
Homo sapiens
Cell type
Mast cell
Cardiac endothelial cell
Cardiac muscle cell
Cardiac ventricle fibroblast
Vascular associated smooth muscle cell
Pericyte
Lymphocyte
Adipocyte
Endothelial cell of lymphatic vessel
Macrophage
Cardiac neuron
Mesothelial cell
Tissue
Developmental stage
Disease
Cardiomyopathy
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
99,457 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of arteriole
+4
Endothelial cell of arteriole
Chorioretinal region
Chorioretinal region
62-year-old stage
+30
62-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell of arteriole
Vein endothelial cell
Endothelial cell of venule
Fenestrated endothelial cell
Endothelial cell of artery
Tissue
Chorioretinal region
Developmental stage
62-year-old stage
27-year-old stage
72-year-old stage
53-year-old stage
21-year-old stage
81-year-old stage
Newborn stage (0-28 days)
82-year-old stage
17-year-old stage
86-year-old stage
30-year-old stage
10-year-old stage
58-year-old stage
90 year-old and over stage
50-year-old stage
64-year-old stage
68-year-old stage
77-year-old stage
11-year-old stage
69-year-old stage
32-year-old stage
63-year-old stage
60-year-old stage
25-year-old stage
46-year-old stage
43-year-old stage
65-year-old stage
71-year-old stage
34-year-old stage
16-year-old stage
47-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
Suspension type
Nucleus
Related Links
celltype.info
CELLxGENE
99,029 cells
•
Bandesh et al., 2025
Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects
Explore
h5ad
Homo sapiens
Homo sapiens
Type b pancreatic cell
Type b pancreatic cell
Islet of langerhans
Islet of langerhans
54-year-old stage
+27
54-year-old stage
Type 2 diabetes mellitus
+2
Type 2 diabetes mellitus
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Type b pancreatic cell
Tissue
Islet of langerhans
Developmental stage
54-year-old stage
35-year-old stage
62-year-old stage
26-year-old stage
53-year-old stage
21-year-old stage
61-year-old stage
57-year-old stage
49-year-old stage
42-year-old stage
52-year-old stage
48-year-old stage
40-year-old stage
38-year-old stage
45-year-old stage
59-year-old stage
30-year-old stage
55-year-old stage
58-year-old stage
50-year-old stage
51-year-old stage
66-year-old stage
32-year-old stage
63-year-old stage
60-year-old stage
25-year-old stage
37-year-old stage
34-year-old stage
Disease
Type 2 diabetes mellitus
Prediabetes syndrome
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
thejacksonlaboratory.shinyapps.io
Zenodo record:14656366
GEO series:GSE221156
CELLxGENE
98,848 cells
•
Phan et al., 2024
Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+9
Astrocyte
Putamen
+1
Putamen
54-year-old stage
+9
54-year-old stage
Opiate dependence
+1
Opiate dependence
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Inhibitory interneuron
Mural cell
Oligodendrocyte precursor cell
Oligodendrocyte
Indirect pathway medium spiny neuron
Medium spiny neuron
Direct pathway medium spiny neuron
Microglial cell
Endothelial cell
Tissue
Putamen
Caudate nucleus
Developmental stage
54-year-old stage
35-year-old stage
39-year-old stage
42-year-old stage
40-year-old stage
41-year-old stage
55-year-old stage
23-year-old stage
60-year-old stage
37-year-old stage
Disease
Opiate dependence
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE233279
CELLxGENE
97,788 cells
•
Kong et al., 2023
The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon
Explore
h5ad
Homo sapiens
Homo sapiens
Enteroendocrine cell
+6
Enteroendocrine cell
Mucosa of transverse colon
+9
Mucosa of transverse colon
Adult stage
+6
Adult stage
Crohn disease
+1
Crohn disease
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Enteroendocrine cell
Enterocyte
Epithelial cell
Tuft cell
Paneth cell
Goblet cell
Stem cell
Tissue
Mucosa of transverse colon
Ascending colon
Sigmoid colon
Colonic epithelium
Cecum mucosa
Caecum epithelium
Descending colon
Mucosa of sigmoid colon
Lamina propria of mucosa of colon
Colon
Developmental stage
Adult stage
Third decade stage
Sixth decade stage
Fourth decade stage
Eighth decade stage
Fifth decade stage
Seventh decade stage
Disease
Crohn disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v1
10x 3' v2
Suspension type
Cell
Related Links
BroadInstitute Single-Cell Portal:SCP1884
HumanCellAtlas:cae461de-ecbd-482f-a5d4-11d607fc12ba
CELLxGENE
97,499 cells
•
Ballestar et al., 2020
Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmablast
+25
Plasmablast
Blood
Blood
Covid-19
Covid-19
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmablast
Mucosal invariant t cell
Cd16-positive, cd56-dim natural killer cell, human
Cd14-low, cd16-positive monocyte
Cd14-positive monocyte
Neutrophil
Cd4-positive, alpha-beta memory t cell
Memory b cell
Plasma cell
Immature b cell
B cell
Gamma-delta t cell
Regulatory t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Hematopoietic stem cell
Plasmacytoid dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Natural killer cell
Platelet
Erythrocyte
Conventional dendritic cell
Mature nk t cell
Cd8-positive, alpha-beta memory t cell
T cell
Naive b cell
Tissue
Blood
Developmental stage
Disease
Covid-19
Sex
Technology
10x 5' v1
Suspension type
Cell
Related Links
protocols.io:purification-of-pbmcs-e6nvw93r2gmk/v1
covid19cellatlas.org
UCSC Cell Browser:covid19-autoimmune-pbmc
HumanCellAtlas:2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba
protocols.io:cite-seq-for-pbmcs-8epv514qjl1b/v1
CELLxGENE
97,125 cells
•
Acera-Mateos et al., 2025
Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas
Explore
h5ad
Homo sapiens
Homo sapiens
Peritubular capillary endothelial cell
+34
Peritubular capillary endothelial cell
Cortex of kidney
Cortex of kidney
74-year-old stage
+14
74-year-old stage
Normal
Normal
Female
+1
Female
10x multiome
+2
10x multiome
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Peritubular capillary endothelial cell
Fibroblast
Epithelial cell of proximal tubule segment 3
Kidney outer medulla collecting duct intercalated cell
Kidney loop of henle thick ascending limb epithelial cell
Renal interstitial pericyte
Parietal epithelial cell
Kidney proximal convoluted tubule epithelial cell
Glomerular capillary endothelial cell
Mast cell
Epithelial cell of proximal tubule
Endothelial cell of arteriole
Podocyte
Vasa recta ascending limb cell
Kidney connecting tubule epithelial cell
Myeloid dendritic cell
Neutrophil
Vasa recta descending limb cell
Plasma cell
Kidney collecting duct alpha-intercalated cell
B cell
Vascular associated smooth muscle cell
Renal beta-intercalated cell
Renal principal cell
Kidney connecting tubule principal cell
Non-classical monocyte
Kidney interstitial alternatively activated macrophage
Plasmacytoid dendritic cell
Kidney loop of henle thin ascending limb epithelial cell
Lymphocyte
Mesangial cell
Endothelial cell of lymphatic vessel
Macula densa epithelial cell
T cell
Epithelial cell of early distal convoluted tubule
Tissue
Cortex of kidney
Developmental stage
74-year-old stage
72-year-old stage
53-year-old stage
57-year-old stage
59-year-old stage
58-year-old stage
50-year-old stage
79-year-old stage
68-year-old stage
69-year-old stage
60-year-old stage
46-year-old stage
67-year-old stage
43-year-old stage
71-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
10x 5' v1
Suspension type
Cell
Nucleus
1
2
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39
40
41
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