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Cell Type
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Tissue
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Disease
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Technology
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Cell
896
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
9,852 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+7
Neutrophil
Respiratory airway
Respiratory airway
49-year-old stage
49-year-old stage
Covid-19
Covid-19
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Erythrocyte
Mature nk t cell
Mast cell
Ionocyte
Epithelial cell
Myeloid cell
B cell
Tissue
Respiratory airway
Developmental stage
49-year-old stage
Disease
Covid-19
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
9,841 cells
•
Ganier et al., 2024
Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma
Explore
h5ad
Homo sapiens
Homo sapiens
Hair follicular keratinocyte
+4
Hair follicular keratinocyte
Skin of abdomen
+7
Skin of abdomen
66-year-old stage
+23
66-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v1
+2
10x 3' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Hair follicular keratinocyte
Basal cell of epidermis
Keratinocyte
Granular cell of epidermis
Sebocyte
Tissue
Skin of abdomen
Scalp
Skin of cheek
Skin of external ear
Skin of forehead
Arm skin
Skin of temple
Nose skin
Developmental stage
66-year-old stage
69-year-old stage
91-year-old stage
85-year-old stage
53-year-old stage
54-year-old stage
39-year-old stage
56-year-old stage
90-year-old stage
80-year-old stage
51-year-old stage
81-year-old stage
24-year-old stage
23-year-old stage
59-year-old stage
25-year-old stage
77-year-old stage
62-year-old stage
86-year-old stage
70-year-old stage
78-year-old stage
63-year-old stage
73-year-old stage
27-year-old stage
Disease
Normal
Basal cell carcinoma
Sex
Female
Male
Technology
10x 3' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
spatial-skin-atlas.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-13084
ArrayExpress BioStudies:E-MTAB-13085
HumanCellAtlas:e49e556a-da5a-442a-b45c-8691b457623e
CELLxGENE
9,816 cells
•
Anderson-Crannage et al., 2023
Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+10
Neutrophil
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
Neutrophil
Endothelial cell
Mast cell
Schwann cell
Fibroblast of lymphatic vessel
Innate lymphoid cell
Keratinocyte
Pericyte
Professional antigen presenting cell
Fibroblast
Chondrocyte
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
9,799 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Chest wall
Chest wall
54-year-old stage
54-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Blood vessel endothelial cell
Blood vessel smooth muscle cell
Macrophage
Malignant cell
Cell of skeletal muscle
Fibroblast
Tissue
Chest wall
Developmental stage
54-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
9,778 cells
•
Chan et al., 2021
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Club cell
+9
Club cell
Pleural effusion
+7
Pleural effusion
69-year-old stage
+24
69-year-old stage
Lung adenocarcinoma
+2
Lung adenocarcinoma
Female
+1
Female
10x 3' transcription profiling
+2
10x 3' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Club cell
Hepatocyte
Pulmonary alveolar epithelial cell
Neuroendocrine cell
Basal cell
Ionocyte
Epithelial cell
Goblet cell
Tuft cell
Ciliated epithelial cell
Tissue
Pleural effusion
Lung
Axilla
Liver
Bone spine
Brain
Adrenal gland
Lymph node
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
71-year-old stage
85-year-old stage
68-year-old stage
44-year-old stage
55-year-old stage
84-year-old stage
82-year-old stage
80-year-old stage
57-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
67-year-old stage
77-year-old stage
64-year-old stage
62-year-old stage
70-year-old stage
78-year-old stage
47-year-old stage
76-year-old stage
79-year-old stage
73-year-old stage
Disease
Lung adenocarcinoma
Normal
Small cell lung carcinoma
Sex
Female
Male
Technology
10x 3' transcription profiling
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
Single Cell Portal
9,740 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+5
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Brain microvascular endothelial cell
Obsolete excitatory neuron
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD720) (section 223)
Corresponding registered brain section (MD720) (section 224)
Corresponding registered brain section (MD720) (section 225)
CELLxGENE
9,705 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+4
Endothelial cell
Forebrain meninges
+2
Forebrain meninges
13th week post-fertilization stage
+8
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell
Epithelial cell
Choroid plexus macrophage
Choroid plexus epithelial cell
Neural progenitor cell
Tissue
Forebrain meninges
Brain meninx
Meninx
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
Carnegie stage 23
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 16
Carnegie stage 18
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
9,675 cells
•
Wu et al., 2021
A single-cell and spatially resolved atlas of human breast cancers
Explore
h5ad
Homo sapiens
Homo sapiens
Macrophage
+2
Macrophage
Breast
Breast
42-year-old stage
+19
42-year-old stage
Invasive ductal breast carcinoma
+2
Invasive ductal breast carcinoma
Female
Female
10x 5' v1
+2
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Macrophage
Myeloid cell
Monocyte
Tissue
Breast
Developmental stage
42-year-old stage
43-year-old stage
85-year-old stage
61-year-old stage
88-year-old stage
52-year-old stage
54-year-old stage
55-year-old stage
82-year-old stage
50-year-old stage
57-year-old stage
49-year-old stage
35-year-old stage
58-year-old stage
67-year-old stage
41-year-old stage
60-year-old stage
63-year-old stage
47-year-old stage
73-year-old stage
Disease
Invasive ductal breast carcinoma
Invasive lobular breast carcinoma
Breast carcinoma
Sex
Female
Technology
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
BroadInstitute Single-Cell Portal:SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers
Github:Swarbricklab-code/BrCa_cell_atlas
GEO series:GSE176078
EGA Study:EGAS00001005173
Zenodo record:4739739
CELLxGENE
9,669 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+10
T cell
Heart
Heart
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Endocardial cell
Cardiac valve cell
Smooth muscle cell
Endothelial cell of coronary artery
Macrophage
B cell
Regular atrial cardiac myocyte
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
9,652 cells
•
Khouri-Farah et al., 2025
Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk
Explore
h5ad
Homo sapiens
Homo sapiens
Peridermal cell
+4
Peridermal cell
Pharyngeal arch system
Pharyngeal arch system
Carnegie stage 14
+5
Carnegie stage 14
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Peridermal cell
Ectodermal cell
Neuroplacodal cell
Epithelial cell of thyroid gland
Pituitary gland cell
Tissue
Pharyngeal arch system
Developmental stage
Carnegie stage 14
Carnegie stage 13
Carnegie stage 20
Carnegie stage 17
Carnegie stage 12
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14343226
Github:cotneylab/craniofacial_snrna
DOI:10.25550/7N-54BY
DOI:10.25550/8D-2JQ0
CELLxGENE
9,626 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+17
Neutrophil
Heart left ventricle
Heart left ventricle
Seventh decade stage
Seventh decade stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neutrophil
Endothelial cell of lymphatic vessel
Mast cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Adipocyte
Cd8-positive, alpha-beta cytotoxic t cell
Macrophage
Glial cell
Plasma cell
Vein endothelial cell
Cd14-positive monocyte
Mesothelial cell
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Heart left ventricle
Developmental stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
9,619 cells
•
Lim et al., 2025
A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary neuroendocrine cell
+4
Pulmonary neuroendocrine cell
Lung
Lung
Normal
Normal
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Pulmonary neuroendocrine cell
Basal cell
Respiratory tract epithelial cell
Lung multiciliated epithelial cell
Pulmonary alveolar type 2 cell
Tissue
Lung
Developmental stage
Disease
Normal
Sex
Technology
10x 5' v1
Suspension type
Cell
Related Links
Github:Peng-He-Lab/2024_AT2_organoids
GEO series:GSE237359
ebi.ac.uk
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