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Technology
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Cell
893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
183
Sort
Most cells
Fewest cells
2343
datasets
CELLxGENE
212,984 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Vascular associated smooth muscle cell
+3
Vascular associated smooth muscle cell
Chorioretinal region
Chorioretinal region
64-year-old stage
+30
64-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Smooth muscle cell
Tissue
Chorioretinal region
Developmental stage
64-year-old stage
50-year-old stage
65-year-old stage
68-year-old stage
82-year-old stage
43-year-old stage
63-year-old stage
90 year-old and over stage
58-year-old stage
34-year-old stage
86-year-old stage
25-year-old stage
11-year-old stage
21-year-old stage
53-year-old stage
46-year-old stage
77-year-old stage
47-year-old stage
32-year-old stage
81-year-old stage
69-year-old stage
Newborn stage (0-28 days)
60-year-old stage
62-year-old stage
16-year-old stage
10-year-old stage
30-year-old stage
72-year-old stage
27-year-old stage
17-year-old stage
71-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
Suspension type
Nucleus
Related Links
celltype.info
CELLxGENE
210,107 cells
•
Vázquez-García et al., 2022
Ovarian cancer mutational processes drive site-specific immune evasion
Explore
h5ad
Homo sapiens
Homo sapiens
Fallopian tube secretory epithelial cell
Fallopian tube secretory epithelial cell
Liver
+18
Liver
80 year-old and over stage
+23
80 year-old and over stage
Malignant ovarian serous tumor
Malignant ovarian serous tumor
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fallopian tube secretory epithelial cell
Tissue
Liver
Diaphragm
Left ovary
Peritoneum
Adnexa of uterus
Large intestine
Urinary bladder
Parietal peritoneum
Fallopian tube
Lymph node
Intestine
Right ovary
Omentum
Abdominal wall
Ascitic fluid
Caecum
Transverse colon
Abdomen
Paracolic gutter
Developmental stage
80 year-old and over stage
64-year-old stage
50-year-old stage
68-year-old stage
41-year-old stage
63-year-old stage
58-year-old stage
75-year-old stage
59-year-old stage
66-year-old stage
61-year-old stage
57-year-old stage
46-year-old stage
56-year-old stage
55-year-old stage
77-year-old stage
78-year-old stage
47-year-old stage
45-year-old stage
70-year-old stage
76-year-old stage
69-year-old stage
60-year-old stage
71-year-old stage
Disease
Malignant ovarian serous tumor
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
dbGaP Study:phs002857
synapse.org:#!Synapse:syn25569736
componcmsk.org
cbioportal.org
Github:shahcompbio/spectrum-tme
GEO series:GSE180661
CELLxGENE
209,126 cells
•
Eraslan et al., 2022
Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function
Explore
h5ad
Homo sapiens
Homo sapiens
Mature nk t cell
+52
Mature nk t cell
Lingula of left lung
+7
Lingula of left lung
Fifth decade stage
+5
Fifth decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mature nk t cell
Epithelial cell of prostate
Professional antigen presenting cell
Melanocyte of skin
Bronchial epithelial cell
Schwann cell
Sebaceous gland cell
Neutrophil
Endothelial cell of lymphatic vessel
Interstitial cell of cajal
Enteric smooth muscle cell
Mast cell
Epithelial cell of sweat gland
Basal-myoepithelial cell of mammary gland
Fibroblast
Squamous epithelial cell
Elicited macrophage
Fibroblast of breast
Endothelial cell of vascular tree
Respiratory basal cell
Macrophage
Dendritic cell
Basal epithelial cell of tracheobronchial tree
T cell
Pulmonary alveolar epithelial cell
Skeletal muscle satellite cell
Slow muscle cell
Epidermal cell
Adipocyte
Basal cell of epidermis
Fibroblast of cardiac tissue
Smooth muscle cell of prostate
Skeletal muscle fiber
Contractile cell
Alveolar macrophage
Skin fibroblast
Glandular secretory epithelial cell
Neuron
Basal epithelial cell of prostatic duct
Myeloid dendritic cell
Subcutaneous adipocyte
Cardiac muscle cell
Cardiac endothelial cell
Neuroendocrine cell
Skeletal muscle fibroblast
Luminal epithelial cell of mammary gland
Smooth muscle cell
Luminal cell of prostate epithelium
B cell
Keratinocyte
Epidermal langerhans cell
Basal cell
Fast muscle cell
Tissue
Lingula of left lung
Breast
Skin of leg
Mucosa
Prostate gland
Esophagus muscularis mucosa
Anterior wall of left ventricle
Gastrocnemius
Developmental stage
Fifth decade stage
Eighth decade stage
Fourth decade stage
Seventh decade stage
Sixth decade stage
Third decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
gtexportal.org
dbGaP Study:phs000424
BroadInstitute Single-Cell Portal:SCP1479/single-nucleus-cross-tissue-molecular-reference-maps
UCSC Cell Browser:cross-tissue-maps
HumanCellAtlas:31887183-a72c-4308-9eac-c6140313f39c
CELLxGENE
208,390 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Breast
Breast
Adult stage
+1
Adult stage
Normal
Normal
Female
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
GEO series:GSE195665
CELLxGENE
207,952 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+27
Natural killer cell
Blood
Blood
82-year-old stage
+6
82-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Activated cd8-positive, alpha-beta t cell
Cd14-positive, cd16-negative classical monocyte
Naive b cell
Regulatory t cell
Cd1c-positive myeloid dendritic cell
Cd4-negative, cd8-negative, alpha-beta intraepithelial t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Memory b cell
Effector cd4-positive, alpha-beta t cell
Activated cd4-positive, alpha-beta t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Gamma-delta t cell
Dendritic cell
Cd14-low, cd16-positive monocyte
Hematopoietic precursor cell
Cd8-positive, alpha-beta memory t cell
Mature b cell
Plasmablast
Cd4-positive, alpha-beta memory t cell
Cd16-negative, cd56-bright natural killer cell, human
Erythroid lineage cell
Platelet
Mucosal invariant t cell
Cd4-positive, alpha-beta cytotoxic t cell
Plasmacytoid dendritic cell
Cd141-positive myeloid dendritic cell
Innate lymphoid cell
Tissue
Blood
Developmental stage
82-year-old stage
63-year-old stage
58-year-old stage
74-year-old stage
77-year-old stage
69-year-old stage
67-year-old stage
Disease
Normal
Open-angle glaucoma
Sex
Female
Male
Technology
10x 5' v2
Suspension type
Cell
Related Links
Github:mcrewcow/PBMC_Glaucoma_human
GEO series:GSE268936
CELLxGENE
205,722 cells
•
Hochbaum et al., 2024
Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration
Explore
h5ad
Mus musculus
Mus musculus
Oligodendrocyte
+21
Oligodendrocyte
Cerebral cortex
Cerebral cortex
Prime adult stage
Prime adult stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Oligodendrocyte
L5/6 near-projecting glutamatergic neuron
L6b glutamatergic cortical neuron
Pericyte
Vascular leptomeningeal cell
Sst gabaergic interneuron
L5 intratelencephalic projecting glutamatergic neuron
L2/3 intratelencephalic projecting glutamatergic neuron
Lamp5 gabaergic interneuron
Pvalb gabaergic interneuron
Perivascular macrophage
L6 corticothalamic-projecting glutamatergic cortical neuron
Oligodendrocyte precursor cell
Sncg gabaergic interneuron
Microglial cell
L4/5 intratelencephalic projecting glutamatergic neuron
L6 intratelencephalic projecting glutamatergic neuron
Endothelial cell
Smooth muscle cell
Vip gabaergic interneuron
L5 extratelencephalic projecting glutamatergic cortical neuron
Astrocyte
Tissue
Cerebral cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE271421
CELLxGENE
205,596 cells
•
Maatz et al., 2025
The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination
Explore
h5ad
Homo sapiens
Homo sapiens
Mast cell
+8
Mast cell
Heart left ventricle
+1
Heart left ventricle
64-year-old stage
+22
64-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mast cell
Cardiac neuron
Mural cell
Myeloid cell
Adipocyte
Lymphocyte
Fibroblast of cardiac tissue
Cardiac muscle cell
Cardiac endothelial cell
Tissue
Heart left ventricle
Apex of heart
Developmental stage
64-year-old stage
26-year-old stage
52-year-old stage
Fifth decade stage
29-year-old stage
24-year-old stage
31-year-old stage
49-year-old stage
25-year-old stage
61-year-old stage
Eighth decade stage
21-year-old stage
55-year-old stage
Seventh decade stage
32-year-old stage
70-year-old stage
19-year-old stage
Sixth decade stage
28-year-old stage
38-year-old stage
30-year-old stage
27-year-old stage
Third decade stage
Disease
Normal
Myocarditis
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Nucleus
Related Links
ENA Project:PRJEB39602
EGA dataset:EGAD00001009292
DOI:10.1126/science.abo1984
DOI:10.1038/s41586-020-2797-4
EGA Study:EGAS50000000769
CELLxGENE
205,153 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
Schwann cell
+2
Schwann cell
Liver
+6
Liver
7-year-old stage
+13
7-year-old stage
Neuroblastoma
Neuroblastoma
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Schwann cell
Neuroblast (sensu vertebrata)
Fibroblast
Tissue
Liver
Lymph node
Neck
Chest
Cervical lymph node
Abdomen
Adrenal gland
Developmental stage
7-year-old stage
16-month-old stage
5-year-old stage
15-month-old stage
3-year-old stage
12-month-old stage
12-year-old stage
2-year-old stage
4-year-old stage
6-month-old stage
20-month-old stage
13-year-old stage
21-month-old stage
18-month-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
203,139 cells
•
Chen et al., 2025
Multi-omic and spatial analysis of mouse kidneys highlights sex-specific differences in gene regulation across the lifespan
Explore
h5ad
Mus musculus
Mus musculus
Metanephric nephron tubule epithelial cell
+20
Metanephric nephron tubule epithelial cell
Kidney
Kidney
21-month-old stage
+5
21-month-old stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Metanephric nephron tubule epithelial cell
Fibroblast
Epithelial cell of proximal tubule segment 2
Kidney collecting duct intercalated cell
Epithelial cell of proximal tubule
Kidney collecting duct principal cell
Macrophage
Epithelial cell of proximal tubule segment 1
T cell
Kidney loop of henle descending limb epithelial cell
Epithelial cell of proximal tubule segment 3
Parietal epithelial cell
Kidney distal convoluted tubule epithelial cell
Kidney loop of henle ascending limb epithelial cell
Conventional dendritic cell
Plasma cell
Ureteric bud cell
Kidney connecting tubule epithelial cell
Endothelial cell
Urothelial cell
Podocyte
Tissue
Kidney
Developmental stage
21-month-old stage
Theiler stage 27
3-6 month-old mature stage
21-day-old stage
12-month-old stage
Theiler stage 24
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
Github:ding-lab/normal_mouse_kidney_scripts
cmowustl.shinyapps.io
GEO series:GSE252772
CELLxGENE
201,575 cells
•
Xu et al., 2023
Automatic cell-type harmonization and integration across Human Cell Atlas datasets
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+18
Endothelial cell of lymphatic vessel
Muscle tissue
+4
Muscle tissue
82-year-old stage
+21
82-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
+4
10x 3' v2
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Cell of skeletal muscle
Capillary endothelial cell
Mast cell
Fibroblast
Mural cell
Pericyte
Tendon cell
Mesenchymal stem cell
Macrophage
Secondary lymphoid organ macrophage
Vein endothelial cell
Slow muscle cell
Adipocyte
Erythroid lineage cell
Lymphocyte
Endothelial cell of artery
Fast muscle cell
Skeletal muscle satellite stem cell
Tissue
Muscle tissue
Rectus abdominis muscle
Skeletal muscle organ, vertebrate
Muscle of abdomen
Muscle of pelvic diaphragm
Developmental stage
82-year-old stage
43-year-old stage
Adult stage
22-year-old stage
75-year-old stage
59-year-old stage
54-year-old stage
61-year-old stage
74-year-old stage
21-year-old stage
77-year-old stage
20-year-old stage
70-year-old stage
81-year-old stage
76-year-old stage
90-year-old stage
62-year-old stage
19-year-old stage
38-year-old stage
79-year-old stage
72-year-old stage
71-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
10x 5' transcription profiling
Smart-seq2
10x 5' v1
Suspension type
Cell
Nucleus
Related Links
ebi.ac.uk
EGA dataset:EGAD00001008575
celltypist.org
Github:ventolab/CVID
teichlab.org
CELLxGENE
201,072 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
Natural killer cell
+16
Natural killer cell
Ileum
+5
Ileum
Fifth decade stage
+5
Fifth decade stage
Normal
+1
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Neutrophil
Cd8-positive, alpha-beta t cell
Regulatory t cell
Mast cell
Monocyte
Macrophage
Dendritic cell
T cell
Naive t cell
Conventional dendritic cell
Plasma cell
Plasmacytoid dendritic cell
Innate lymphoid cell
Cd4-positive, alpha-beta t cell
B cell
Intraepithelial lymphocyte
Tissue
Ileum
Ileal epithelium
Lamina propria of small intestine
Small intestine
Ileum lamina propria
Epithelium of small intestine
Developmental stage
Fifth decade stage
Eighth decade stage
Fourth decade stage
Seventh decade stage
Sixth decade stage
Third decade stage
Disease
Normal
Crohn disease
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
HumanCellAtlas:cae461de-ecbd-482f-a5d4-11d607fc12ba
BroadInstitute Single-Cell Portal:SCP1884
CELLxGENE
200,664 cells
•
Xu et al., 2023
Automatic cell-type harmonization and integration across Human Cell Atlas datasets
Explore
h5ad
Homo sapiens
Homo sapiens
Megakaryocyte
+30
Megakaryocyte
Spleen
Spleen
Fifth decade stage
+8
Fifth decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
+5
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Megakaryocyte
Dendritic cell, human
Non-classical monocyte
Erythrocyte
Neutrophil
Naive b cell
Classical monocyte
Regulatory t cell
Mast cell
Leukocyte
Memory b cell
Macrophage
Gamma-delta t cell
Hematopoietic multipotent progenitor cell
Central memory cd4-positive, alpha-beta t cell
Plasmablast
Cd16-negative, cd56-bright natural killer cell, human
Erythroid lineage cell
Conventional dendritic cell
Plasma cell
Central memory cd8-positive, alpha-beta t cell
Effector memory cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Plasmacytoid dendritic cell
Effector memory cd8-positive, alpha-beta t cell, terminally differentiated
Endothelial cell
Innate lymphoid cell
Cd16-positive, cd56-dim natural killer cell, human
T follicular helper cell
Effector memory cd8-positive, alpha-beta t cell
B cell
Tissue
Spleen
Developmental stage
Fifth decade stage
31-year-old stage
59-year-old stage
61-year-old stage
Eighth decade stage
Seventh decade stage
69-year-old stage
Sixth decade stage
Third decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
10x 5' transcription profiling
10x 5' v2
Smart-seq2
10x 5' v1
Suspension type
Cell
Related Links
ebi.ac.uk
EGA dataset:EGAD00001008575
celltypist.org
Github:ventolab/CVID
teichlab.org
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