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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
212,984 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Smooth muscle cell
+3
Smooth muscle cell
Chorioretinal region
Chorioretinal region
69-year-old stage
+30
69-year-old stage
Normal
Normal
Female
+1
Female
10x 5' v2
+1
10x 5' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Smooth muscle cell
Pericyte
Vascular associated smooth muscle cell
Fibroblast
Tissue
Chorioretinal region
Developmental stage
69-year-old stage
21-year-old stage
34-year-old stage
65-year-old stage
43-year-old stage
71-year-old stage
53-year-old stage
68-year-old stage
30-year-old stage
17-year-old stage
82-year-old stage
50-year-old stage
72-year-old stage
81-year-old stage
16-year-old stage
58-year-old stage
25-year-old stage
90 year-old and over stage
32-year-old stage
77-year-old stage
64-year-old stage
62-year-old stage
86-year-old stage
46-year-old stage
60-year-old stage
Newborn stage (0-28 days)
63-year-old stage
47-year-old stage
11-year-old stage
27-year-old stage
10-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v3
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
Ascitic fluid
+18
Ascitic fluid
66-year-old stage
+23
66-year-old 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
Ascitic fluid
Diaphragm
Caecum
Peritoneum
Parietal peritoneum
Left ovary
Liver
Abdomen
Urinary bladder
Intestine
Right ovary
Adnexa of uterus
Fallopian tube
Large intestine
Transverse colon
Omentum
Paracolic gutter
Abdominal wall
Lymph node
Developmental stage
66-year-old stage
69-year-old stage
75-year-old stage
71-year-old stage
61-year-old stage
68-year-old stage
56-year-old stage
55-year-old stage
50-year-old stage
57-year-old stage
80 year-old and over stage
58-year-old stage
59-year-old stage
77-year-old stage
64-year-old stage
45-year-old stage
41-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
78-year-old stage
63-year-old stage
47-year-old stage
76-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
GEO series:GSE180661
componcmsk.org
cbioportal.org
Github:shahcompbio/spectrum-tme
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
Fast muscle cell
+52
Fast muscle cell
Mucosa
+7
Mucosa
Sixth decade stage
+5
Sixth decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fast muscle cell
T cell
Neutrophil
Epidermal langerhans cell
Cardiac endothelial cell
Luminal cell of prostate epithelium
Endothelial cell of lymphatic vessel
Pulmonary alveolar epithelial cell
Slow muscle cell
Neuroendocrine cell
Mature nk t cell
Epithelial cell of prostate
Interstitial cell of cajal
Mast cell
Contractile cell
Basal cell
Luminal epithelial cell of mammary gland
Schwann cell
Smooth muscle cell
Skeletal muscle satellite cell
Bronchial epithelial cell
Myeloid dendritic cell
Endothelial cell of vascular tree
Adipocyte
Basal cell of epidermis
Epithelial cell of sweat gland
Macrophage
Enteric smooth muscle cell
Skin fibroblast
Subcutaneous adipocyte
Basal-myoepithelial cell of mammary gland
Respiratory basal cell
Fibroblast of breast
Keratinocyte
Smooth muscle cell of prostate
Alveolar macrophage
Basal epithelial cell of prostatic duct
Sebaceous gland cell
Glandular secretory epithelial cell
Squamous epithelial cell
Epidermal cell
Cardiac muscle cell
B cell
Melanocyte of skin
Professional antigen presenting cell
Neuron
Skeletal muscle fibroblast
Elicited macrophage
Fibroblast
Dendritic cell
Fibroblast of cardiac tissue
Basal epithelial cell of tracheobronchial tree
Skeletal muscle fiber
Tissue
Mucosa
Esophagus muscularis mucosa
Breast
Gastrocnemius
Skin of leg
Lingula of left lung
Anterior wall of left ventricle
Prostate gland
Developmental stage
Sixth decade stage
Fifth decade stage
Third decade stage
Seventh decade stage
Fourth decade stage
Eighth 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' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Breast
Developmental stage
Adult stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
Github:navinlabcode/HumanBreastCellAtlas
GEO series:GSE195665
CELLxGENE
207,952 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Cd1c-positive myeloid dendritic cell
+27
Cd1c-positive myeloid dendritic cell
Blood
Blood
69-year-old stage
+6
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Cd1c-positive myeloid dendritic cell
Natural killer cell
Cd4-negative, cd8-negative, alpha-beta intraepithelial t cell
Gamma-delta t cell
Activated cd4-positive, alpha-beta t cell
Hematopoietic precursor cell
Platelet
Cd141-positive myeloid dendritic cell
Erythroid lineage cell
Plasmacytoid dendritic cell
Effector cd4-positive, alpha-beta t cell
Cd8-positive, alpha-beta memory t cell
Cd4-positive, alpha-beta cytotoxic t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Memory b cell
Innate lymphoid cell
Regulatory t cell
Mature b cell
Activated cd8-positive, alpha-beta t cell
Plasmablast
Cd14-low, cd16-positive monocyte
Cd4-positive, alpha-beta memory t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Cd14-positive, cd16-negative classical monocyte
Naive b cell
Dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Tissue
Blood
Developmental stage
69-year-old stage
82-year-old stage
74-year-old stage
58-year-old stage
67-year-old stage
77-year-old stage
63-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
L2/3 intratelencephalic projecting glutamatergic neuron
+21
L2/3 intratelencephalic projecting glutamatergic neuron
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
L2/3 intratelencephalic projecting glutamatergic neuron
L5/6 near-projecting glutamatergic neuron
Oligodendrocyte precursor cell
L5 intratelencephalic projecting glutamatergic neuron
L4/5 intratelencephalic projecting glutamatergic neuron
Endothelial cell
Oligodendrocyte
Vascular leptomeningeal cell
Smooth muscle cell
Lamp5 gabaergic interneuron
Microglial cell
Vip gabaergic interneuron
L5 extratelencephalic projecting glutamatergic cortical neuron
L6b glutamatergic cortical neuron
L6 corticothalamic-projecting glutamatergic cortical neuron
Pvalb gabaergic interneuron
Pericyte
Perivascular macrophage
L6 intratelencephalic projecting glutamatergic neuron
Sncg gabaergic interneuron
Astrocyte
Sst gabaergic interneuron
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
Cardiac endothelial cell
+8
Cardiac endothelial cell
Apex of heart
+1
Apex of heart
21-year-old stage
+22
21-year-old stage
Myocarditis
+1
Myocarditis
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cardiac endothelial cell
Mast cell
Cardiac neuron
Lymphocyte
Adipocyte
Mural cell
Myeloid cell
Cardiac muscle cell
Fibroblast of cardiac tissue
Tissue
Apex of heart
Heart left ventricle
Developmental stage
21-year-old stage
26-year-old stage
Sixth decade stage
61-year-old stage
52-year-old stage
30-year-old stage
29-year-old stage
38-year-old stage
Fifth decade stage
55-year-old stage
28-year-old stage
Third decade stage
49-year-old stage
24-year-old stage
Seventh decade stage
25-year-old stage
32-year-old stage
64-year-old stage
70-year-old stage
31-year-old stage
19-year-old stage
Eighth decade stage
27-year-old stage
Disease
Myocarditis
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
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
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
Schwann cell
Neuroblast (sensu vertebrata)
Fibroblast
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
Zenodo record:14261274
dbGaP Study:phs002371
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
T cell
+20
T cell
Kidney
Kidney
Theiler stage 27
+5
Theiler stage 27
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Mus musculus
Cell type
T cell
Podocyte
Parietal epithelial cell
Endothelial cell
Kidney collecting duct intercalated cell
Ureteric bud cell
Epithelial cell of proximal tubule
Metanephric nephron tubule epithelial cell
Epithelial cell of proximal tubule segment 1
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule epithelial cell
Urothelial cell
Epithelial cell of proximal tubule segment 3
Plasma cell
Epithelial cell of proximal tubule segment 2
Kidney loop of henle descending limb epithelial cell
Kidney loop of henle ascending limb epithelial cell
Conventional dendritic cell
Fibroblast
Tissue
Kidney
Developmental stage
Theiler stage 27
12-month-old stage
21-day-old stage
Theiler stage 24
21-month-old stage
3-6 month-old mature stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
GEO series:GSE252772
Github:ding-lab/normal_mouse_kidney_scripts
cmowustl.shinyapps.io
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
Fast muscle cell
+18
Fast muscle cell
Muscle tissue
+4
Muscle tissue
75-year-old stage
+21
75-year-old stage
Normal
Normal
Female
+1
Female
10x 5' transcription profiling
+4
10x 5' transcription profiling
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Fast muscle cell
Endothelial cell of lymphatic vessel
Slow muscle cell
Mast cell
Tendon cell
Erythroid lineage cell
Endothelial cell of artery
Capillary endothelial cell
Lymphocyte
Adipocyte
Macrophage
Mural cell
Secondary lymphoid organ macrophage
Vein endothelial cell
Cell of skeletal muscle
Pericyte
Skeletal muscle satellite stem cell
Mesenchymal stem cell
Fibroblast
Tissue
Muscle tissue
Skeletal muscle organ, vertebrate
Muscle of pelvic diaphragm
Rectus abdominis muscle
Muscle of abdomen
Developmental stage
75-year-old stage
21-year-old stage
43-year-old stage
71-year-old stage
61-year-old stage
54-year-old stage
38-year-old stage
82-year-old stage
90-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
59-year-old stage
Adult stage
77-year-old stage
62-year-old stage
70-year-old stage
22-year-old stage
19-year-old stage
20-year-old stage
76-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' transcription profiling
10x 5' v1
Smart-seq2
10x 3' v3
10x 3' v2
Suspension type
Cell
Nucleus
Related Links
ebi.ac.uk
celltypist.org
Github:ventolab/CVID
teichlab.org
EGA dataset:EGAD00001008575
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
T cell
+16
T cell
Ileal epithelium
+5
Ileal epithelium
Sixth decade stage
+5
Sixth decade stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Neutrophil
Natural killer cell
Mast cell
Cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Macrophage
Innate lymphoid cell
Regulatory t cell
Intraepithelial lymphocyte
Plasma cell
Cd4-positive, alpha-beta t cell
B cell
Naive t cell
Monocyte
Conventional dendritic cell
Dendritic cell
Tissue
Ileal epithelium
Small intestine
Ileum
Ileum lamina propria
Lamina propria of small intestine
Epithelium of small intestine
Developmental stage
Sixth decade stage
Fifth decade stage
Third decade stage
Seventh decade stage
Fourth decade stage
Eighth decade stage
Disease
Normal
Crohn disease
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
BroadInstitute Single-Cell Portal:SCP1884
HumanCellAtlas:cae461de-ecbd-482f-a5d4-11d607fc12ba
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
Central memory cd4-positive, alpha-beta t cell
+30
Central memory cd4-positive, alpha-beta t cell
Spleen
Spleen
69-year-old stage
+8
69-year-old stage
Normal
Normal
Female
+1
Female
10x 5' v2
+5
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Central memory cd4-positive, alpha-beta t cell
Neutrophil
Dendritic cell, human
Erythrocyte
Gamma-delta t cell
Endothelial cell
Mast cell
Effector memory cd4-positive, alpha-beta t cell
Erythroid lineage cell
Leukocyte
Classical monocyte
Plasmacytoid dendritic cell
Macrophage
Effector memory cd8-positive, alpha-beta t cell, terminally differentiated
Memory b cell
Cd16-positive, cd56-dim natural killer cell, human
Innate lymphoid cell
Regulatory t cell
Plasmablast
Plasma cell
Hematopoietic multipotent progenitor cell
Megakaryocyte
T follicular helper cell
B cell
Mucosal invariant t cell
Central memory cd8-positive, alpha-beta t cell
Naive b cell
Conventional dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Effector memory cd8-positive, alpha-beta t cell
Non-classical monocyte
Tissue
Spleen
Developmental stage
69-year-old stage
Sixth decade stage
61-year-old stage
Fifth decade stage
Third decade stage
Seventh decade stage
59-year-old stage
31-year-old stage
Eighth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' transcription profiling
10x 5' v1
Smart-seq2
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
ebi.ac.uk
celltypist.org
Github:ventolab/CVID
teichlab.org
EGA dataset:EGAD00001008575
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2
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25
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