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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
9,615 cells
•
Choksi et al., 2024
An alternative cell cycle coordinates multiciliated cell differentiation
Explore
h5ad
Mus musculus
Mus musculus
Tracheal epithelial cell
Tracheal epithelial cell
Tracheal epithelial cell
Tracheal epithelial cell
Mature stage
Mature stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Tracheal epithelial cell
Tissue
Tracheal epithelial cell
Developmental stage
Mature stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE228110
Zenodo record:10896100
Zenodo record:10896066
Zenodo record:10896071
Github:lb15/multiciliation_cycle
CELLxGENE
9,563 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
Mus musculus
Mus musculus
Peridermal cell
+5
Peridermal cell
Pharyngeal arch system
Pharyngeal arch system
Theiler stage 22
+5
Theiler stage 22
Normal
Normal
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Peridermal cell
Ectodermal cell
Neuroplacodal cell
Myeloid cell
Pituitary gland cell
Mesenchymal cell
Tissue
Pharyngeal arch system
Developmental stage
Theiler stage 22
Theiler stage 17
Theiler stage 19
Theiler stage 20
Theiler stage 21
Theiler stage 23
Disease
Normal
Sex
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14343226
DOI:10.25550/8D-2JQ0
DOI:10.25550/7N-54BY
Github:cotneylab/craniofacial_snrna
CELLxGENE
9,471 cells
•
Wiedemann et al., 2023
Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin
Explore
h5ad
Homo sapiens
Homo sapiens
Keratinocyte
Keratinocyte
Skin of body
+1
Skin of body
65-year-old stage
+3
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Keratinocyte
Tissue
Skin of body
Skin epidermis
Developmental stage
65-year-old stage
39-year-old stage
56-year-old stage
40-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
skingenes.org
GEO series:GSE202352
HumanCellAtlas:da74b507-60ee-4dd1-bd02-807bb051a337
CELLxGENE
9,446 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Caudal ganglionic eminence derived interneuron
Caudal ganglionic eminence derived interneuron
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
69-year-old stage
+20
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Caudal ganglionic eminence derived interneuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
69-year-old stage
75-year-old stage
42-year-old stage
89-year-old stage
87-year-old stage
85-year-old stage
88-year-old stage
68-year-old stage
29-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
80-year-old stage
72-year-old stage
81-year-old stage
80 year-old and over stage
77-year-old stage
86-year-old stage
70-year-old stage
78-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
Adult Changes in Thought Study
BRaIN-lab
Allen Brain Map:seattle-alzheimers-disease
AWS Open Data:allen-sea-ad-atlas
Alzheimer's Disease Research Center
AD knowledge portal:syn26223298
CELLxGENE
9,422 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of hepatic sinusoid
+5
Endothelial cell of hepatic sinusoid
Caudate lobe of liver
Caudate lobe of liver
Late adult stage
+2
Late adult stage
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of hepatic sinusoid
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Endothelial cell of artery
Endothelial cell of pericentral hepatic sinusoid
Vein endothelial cell
Tissue
Caudate lobe of liver
Developmental stage
Late adult stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE247128
GEO series:GSE245620
GEO series:GSE243977
CELLxGENE
9,422 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
Blood vessel endothelial cell
+7
Blood vessel endothelial cell
Liver
Liver
46-year-old stage
46-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Blood vessel endothelial cell
Endothelial cell
Mature nk t cell
Blood vessel smooth muscle cell
Macrophage
Malignant cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
46-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
9,409 cells
•
Travaglini et al., 2020
A molecular cell atlas of the human lung from single-cell RNA sequencing
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+39
Neutrophil
Lung
+1
Lung
75-year-old stage
+2
75-year-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Club cell
Cd1c-positive myeloid dendritic cell
Dendritic cell, human
Natural killer cell
Endothelial cell of lymphatic vessel
Endothelial cell
Mature nk t cell
Pulmonary ionocyte
Pulmonary neuroendocrine cell
Basal cell
Effector memory cd4-positive, alpha-beta t cell
Lung goblet cell
Endothelial cell of artery
Capillary endothelial cell
Classical monocyte
Intermediate monocyte
Plasmacytoid dendritic cell, human
Epithelial cell
Lung multiciliated epithelial cell
Lymphocyte
Naive thymus-derived cd8-positive, alpha-beta t cell
Pulmonary alveolar type 1 cell
Bronchial smooth muscle cell
Respiratory basal cell
Alveolar macrophage
Plasma cell
Vein endothelial cell
Pulmonary interstitial fibroblast
B cell
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Myeloid leukocyte
Vascular associated smooth muscle cell
Myofibroblast cell
Fibroblast
Dendritic cell
Pulmonary alveolar type 2 cell
Effector memory cd8-positive, alpha-beta t cell
Non-classical monocyte
Tissue
Lung
Blood
Developmental stage
75-year-old stage
51-year-old stage
46-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
EGA Study:EGAS00001004344
ncbi.nlm.nih.gov
CZ BioHub Portal:hlca
synapse.org:#!Synapse:syn21041850/wiki/600865
Github:krasnowlab/HLCA
UCSC Cell Browser:stanford-czb-hlca
HumanCellAtlas:6936da41-3692-46bb-bca1-cd0f507991e9
Single Cell Portal
9,391 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+2
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Brain microvascular endothelial cell
Obsolete excitatory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD736) (section 112)
Corresponding registered brain section (MD736) (section 113)
Corresponding registered brain section (MD736) (section 115)
CELLxGENE
9,362 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
Slide-seqv2
Slide-seqv2
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
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
9,354 cells
•
Gong et al., 2025
Multi-omic profiling reveals age-related immune dynamics in healthy adults
Explore
h5ad
Homo sapiens
Homo sapiens
Erythrocyte
+4
Erythrocyte
Blood
Blood
66-year-old stage
+50
66-year-old stage
Cytomegalovirus infection
+1
Cytomegalovirus infection
Female
+1
Female
10x gene expression flex
10x gene expression flex
Cell
Cell
Organism
Homo sapiens
Cell type
Erythrocyte
Platelet
Basophil mast progenitor cell
Common myeloid progenitor
Common lymphoid progenitor
Tissue
Blood
Developmental stage
66-year-old stage
69-year-old stage
75-year-old stage
65-year-old stage
42-year-old stage
89-year-old stage
43-year-old stage
87-year-old stage
71-year-old stage
85-year-old stage
53-year-old stage
61-year-old stage
88-year-old stage
52-year-old stage
54-year-old stage
68-year-old stage
48-year-old stage
44-year-old stage
56-year-old stage
55-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
80-year-old stage
51-year-old stage
57-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
80 year-old and over stage
49-year-old stage
58-year-old stage
59-year-old stage
67-year-old stage
77-year-old stage
64-year-old stage
45-year-old stage
62-year-old stage
86-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
79-year-old stage
73-year-old stage
83-year-old stage
40-year-old stage
Disease
Cytomegalovirus infection
Normal
Sex
Female
Male
Technology
10x gene expression flex
Suspension type
Cell
Related Links
apps.allenimmunology.org
GEO series:GSE275067
CELLxGENE collection:e9360edf-b0b7-4e01-bce8-e596814f13e7
CELLxGENE
9,337 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
+6
Neutrophil
Blood
Blood
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
Mature nk t cell
Platelet
Myeloid cell
Plasma cell
B cell
Dendritic cell
Tissue
Blood
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
COVID-19 cell atlas
Github:simslab/cluster_diffex2018
CELLxGENE
9,286 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Glioblast (sensu vertebrata)
+15
Glioblast (sensu vertebrata)
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
Glioblast (sensu vertebrata)
Oligodendrocyte precursor cell
Retinal ganglion cell
Epithelial cell
Forebrain neuroblast
Forebrain radial glial cell
Neuroblast (sensu vertebrata)
Radial glial cell
Pinealocyte
Interneuron
Choroid plexus epithelial cell
Spinal cord radial glial cell
Neuron
Retinal cell
Neuronal-restricted precursor
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
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