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Cell
871
Nucleus
653
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Asap
43
Bgee
40
Cellxgene
2,045
Single cell portal
176
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Most cells
Fewest cells
2304
datasets
CELLxGENE
117,346 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+9
Fibroblast
Breast
Breast
Adult stage
+1
Adult stage
Normal
Normal
Female
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Luminal epithelial cell of mammary gland
Endothelial cell of vascular tree
Myeloid cell
Mast cell
Adipocyte of breast
Pericyte
Endothelial cell of lymphatic vessel
Basal cell
T cell
Tissue
Breast
Developmental stage
Adult stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
GEO series:GSE195665
CELLxGENE
117,266 cells
•
Lee et al., 2026
Defining the cellular and molecular identities of histologic subtypes in lung adenocarcinoma
Explore
h5ad
Homo sapiens
Homo sapiens
Innate lymphoid cell
+20
Innate lymphoid cell
Lung parenchyma
Lung parenchyma
78-year-old stage
+13
78-year-old stage
Lung adenocarcinoma
Lung adenocarcinoma
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Innate lymphoid cell
Lung pericyte
Mast cell
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Neutrophil
Plasma cell
B cell
Gamma-delta t cell
Fibroblast of lung
Epithelial cell of lung
Plasmacytoid dendritic cell
Lymphocyte
Cd8-positive, alpha-beta t cell
Lung macrophage
Natural killer cell
Macrophage
Cycling mononuclear phagocyte
Conventional dendritic cell
Monocyte
Cd4-positive, alpha-beta t cell
Endothelial cell
Tissue
Lung parenchyma
Developmental stage
78-year-old stage
73-year-old stage
72-year-old stage
70-year-old stage
58-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
69-year-old stage
76-year-old stage
63-year-old stage
60-year-old stage
56-year-old stage
67-year-old stage
Disease
Lung adenocarcinoma
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
117,094 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+7
Fibroblast
Stomach
+5
Stomach
Carnegie stage 19
+10
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Smooth muscle cell
Interstitial cell of cajal
Pericyte
Angiogenic pericyte
Mesodermal cell
Gastrointestinal tract (lamina propria) macrophage
Mesothelial cell
Tissue
Stomach
Ileum
Small intestine
Jejunum
Duodenum
Colon
Developmental stage
Carnegie stage 19
Carnegie stage 18
10th week post-fertilization stage
Embryonic stage
Carnegie stage 22
11th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 17
9th week post-fertilization stage
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
10x 3' v2
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
116,778 cells
•
Long et al., 2024
Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary alveolar epithelial cell
+21
Pulmonary alveolar epithelial cell
Lung
Lung
35-year-old stage
+12
35-year-old stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Pulmonary alveolar epithelial cell
Smooth muscle cell
Lymphatic endothelial cell of trabecula
Dendritic cell
B cell
Fibroblast of lung
Pulmonary capillary endothelial cell
Myofibroblast cell
Club cell
Pulmonary alveolar type 2 cell
Goblet cell
Respiratory basal cell
Pulmonary alveolar type 1 cell
Cd16-negative, cd56-bright natural killer cell, human
Natural killer cell
Macrophage
Ciliated cell
Monocyte
Vein endothelial cell of respiratory system
Mesothelial cell
T cell
Endothelial cell of artery
Tissue
Lung
Developmental stage
35-year-old stage
62-year-old stage
72-year-old stage
61-year-old stage
40-year-old stage
50-year-old stage
51-year-old stage
68-year-old stage
66-year-old stage
31-year-old stage
60-year-old stage
71-year-old stage
44-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
GEO series:GSE241468
Github:pumclyy/HLISCA
Zenodo record:13306592
CELLxGENE
116,576 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+10
Fibroblast
Primary motor cortex
Primary motor cortex
42-year-old stage
+3
42-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular associated smooth muscle cell
Pericyte
Leukocyte
Central nervous system macrophage
Choroid plexus epithelial cell
Neuron
Endothelial cell
Tissue
Primary motor cortex
Developmental stage
42-year-old stage
50-year-old stage
29-year-old stage
60-year-old stage
Disease
Normal
Sex
Female
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
116,313 cells
•
Melms et al., 2021
A molecular single-cell lung atlas of lethal COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+29
Fibroblast
Lung
Lung
78-year-old stage
+14
78-year-old stage
Covid-19
+1
Covid-19
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Mast cell
Vein endothelial cell
Mesothelial fibroblast
Alveolar macrophage
Epithelial cell
Plasma cell
Dendritic cell
B cell
Regulatory t cell
Tracheobronchial smooth muscle cell
Vascular associated smooth muscle cell
Capillary endothelial cell
Mucus secreting cell
Pericyte
Club cell
Pulmonary alveolar type 2 cell
Lung goblet cell
Respiratory basal cell
Alveolar adventitial fibroblast
Cd8-positive, alpha-beta t cell
Natural killer cell
Macrophage
Monocyte
Cd4-positive, alpha-beta t cell
Lung multiciliated epithelial cell
Neuron
Brush cell of tracheobronchial tree
Endothelial cell
Endothelial cell of artery
Tissue
Lung
Developmental stage
78-year-old stage
73-year-old stage
72-year-old stage
83-year-old stage
70-year-old stage
58-year-old stage
75-year-old stage
79-year-old stage
68-year-old stage
69-year-old stage
63-year-old stage
80-year-old stage
84-year-old stage
65-year-old stage
71-year-old stage
Disease
Covid-19
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
BroadInstitute Single-Cell Portal:SCP1219/columbia-university-nyp-covid-19-lung-atlas#
GEO series:GSE171524
UCSC Cell Browser:covid19-cellular-targets
HumanCellAtlas:d7845650-f6b1-4b1c-b2fe-c0795416ba7b
CELLxGENE
116,142 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Pvalb gabaergic interneuron
Pvalb 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
Pvalb 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
Allen Brain Map:seattle-alzheimers-disease
AWS Open Data:allen-sea-ad-atlas
AD knowledge portal:syn26223298
CELLxGENE
115,788 cells
•
Rustam et al., 2023
A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+42
Fibroblast
Bronchus
+2
Bronchus
39-year-old stage
+15
39-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Pulmonary ionocyte
Schwann cell
Multiciliated columnar cell of tracheobronchial tree
Mast cell
Bronchus fibroblast of lung
Neutrophil
Lung microvascular endothelial cell
Respiratory tract goblet cell
Lung resident memory cd8-positive, alpha-beta t cell
Plasma cell
B cell
Chondrocyte
Serous secreting cell of bronchus submucosal gland
Bronchiolar smooth muscle cell
Vascular associated smooth muscle cell
Fibroblast of lung
Serous cell of epithelium of lobular bronchiole
Pulmonary capillary endothelial cell
Pericyte
Pulmonary alveolar type 2 cell
Plasmacytoid dendritic cell
Myoepithelial cell of bronchus submucosal gland
Respiratory basal cell
Tracheobronchial serous cell
Cd8-positive, alpha-beta t cell
Pulmonary alveolar type 1 cell
Blood vessel smooth muscle cell
Endothelial cell of lymphatic vessel
Natural killer cell
Macrophage
Deuterosomal cell
Alternatively activated macrophage
Conventional dendritic cell
Monocyte
Mature nk t cell
Vein endothelial cell of respiratory system
Cd4-positive, alpha-beta t cell
T cell
Respiratory tract suprabasal cell
Pulmonary neuroendocrine cell
Mucus secreting cell of bronchus submucosal gland
Endothelial cell of artery
Tissue
Bronchus
Terminal bronchus
Segmental bronchus
Developmental stage
39-year-old stage
61-year-old stage
57-year-old stage
12-year-old stage
41-year-old stage
58-year-old stage
66-year-old stage
11-year-old stage
32-year-old stage
63-year-old stage
56-year-old stage
37-year-old stage
24-year-old stage
67-year-old stage
20-year-old stage
65-year-old stage
Disease
Normal
Chronic obstructive pulmonary disease
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Single Cell Portal
115,569 cells
•
Ziegler et al., 2020
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Explore
Homo sapiens
Homo sapiens
Iga plasma cell
+10
Iga plasma cell
Functional gastric disease
Functional gastric disease
10x 3' v2
10x 3' v2
Organism
Homo sapiens
Cell type
Iga plasma cell
Fibroblast
Mast cell
Igg plasma cell
Glial cell
Gut endothelial cell
Epithelial cell
B cell
Myeloid leukocyte
Igm plasma cell
T cell
Tissue
Developmental stage
Disease
Functional gastric disease
Sex
Technology
10x 3' v2
Suspension type
Related Links
cellxgene.cziscience.com
cellxgene.cziscience.com
CELLxGENE
115,548 cells
•
Reichart et al., 2022
Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
Endothelial cell
Heart left ventricle
+3
Heart left ventricle
Third decade stage
+7
Third decade stage
Non-compaction cardiomyopathy
+3
Non-compaction cardiomyopathy
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell
Tissue
Heart left ventricle
Apex of heart
Interventricular septum
Heart right ventricle
Developmental stage
Third decade stage
Postnatal stage
Sixth decade stage
Fourth decade stage
Eighth decade stage
Fifth decade stage
Pediatric stage
Seventh decade stage
Disease
Non-compaction cardiomyopathy
Arrhythmogenic right ventricular cardiomyopathy
Dilated cardiomyopathy
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
Zenodo record:6962685#.YuyuihxBzKE
EGA Study:EGAS00001006374
Github:heiniglab/DCM_heart_cell_atlas
CELLxGENE
115,282 cells
•
Sepp et al., 2023
Cellular development and evolution of the mammalian cerebellum
Explore
h5ad
Mus musculus
Mus musculus
Neuroblast (sensu vertebrata)
+20
Neuroblast (sensu vertebrata)
Cerebellar hemisphere
+1
Cerebellar hemisphere
2-month-old stage
+10
2-month-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Neuroblast (sensu vertebrata)
Cerebellar granule cell
Gabaergic neuron
Immature astrocyte
Glioblast
Noradrenergic cell
Oligodendrocyte
Purkinje cell
Bergmann glial cell
Motor neuron
Brain vascular cell
Erythroid lineage cell
Unipolar brush cell
Interneuron
Ependymal cell
Glutamatergic neuron
Central nervous system macrophage
Cerebellar granule cell precursor
Meningeal macrophage
Microglial cell
Macroglial cell
Tissue
Cerebellar hemisphere
Cerebellum
Developmental stage
2-month-old stage
Theiler stage 18
7-day-old stage
4-day-old stage
Theiler stage 23
Theiler stage 20
Theiler stage 22
Theiler stage 21
Theiler stage 25
Theiler stage 27
2-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
home.kaessmannlab.org
DOI:10.11588/data/QDOC4E
apps.kaessmannlab.org
gitlab.com
Single Cell Portal
114,805 cells
Explore
Mus musculus
Mus musculus
Cell
Cell
Normal
Normal
Mixed sex
Mixed sex
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Cell
Tissue
Developmental stage
Disease
Normal
Sex
Mixed sex
Technology
10x 3' v2
Suspension type
1
2
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