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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
9,275 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Immature t cell
+5
Immature t cell
Thymus
Thymus
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Immature t cell
Dn3 thymocyte
Thymocyte
Dn4 thymocyte
Professional antigen presenting cell
Double negative thymocyte
Tissue
Thymus
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
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
9,263 cells
•
Matuck et al., 2026
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+17
Neutrophil
Hard palate
+1
Hard palate
34-year-old stage
+2
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Merkel cell
Blood vessel endothelial cell
Natural killer cell
Endothelial cell of lymphatic vessel
Mast cell
Cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Schwann cell
Melanocyte
Macrophage
Mural cell
Keratinocyte
Plasma cell
Langerhans cell
B cell
Fibroblast
Dendritic cell
Tissue
Hard palate
Soft palate
Developmental stage
34-year-old stage
Seventh decade stage
32-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:Loci-lab/Oral-Craniofacial-Atlas
CELLxGENE
9,257 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Gabaergic neuron
Gabaergic neuron
Primary motor cortex
Primary motor cortex
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
Github:AllenInstitute/BICCN_M1_Evo
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
CELLxGENE
9,249 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Mus musculus
Mus musculus
Gabaergic neuron
Gabaergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
CELLxGENE
9,203 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
Middle temporal gyrus
Middle temporal gyrus
69-year-old stage
+23
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
Middle temporal gyrus
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
89-year-old stage
43-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
Adult stage
77-year-old stage
86-year-old stage
70-year-old stage
60-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
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
AD knowledge portal:syn26223298
AWS Open Data:allen-sea-ad-atlas
Allen Brain Map:seattle-alzheimers-disease
CELLxGENE
9,156 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Brodmann (1909) area 13
+87
Brodmann (1909) area 13
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
Tissue
Brodmann (1909) area 13
Brodmann (1909) area 14
Brodmann (1909) area 19
Brodmann (1909) area 23
Brodmann (1909) area 24
Brodmann (1909) area 25
Brodmann (1909) area 32
Brodmann (1909) area 35
Brodmann (1909) area 38
Brodmann (1909) area 40
Brodmann (1909) area 43
Brodmann (1909) area 46
Accessory basal amygdaloid nucleus
Agranular insular cortex
Anterior cortical amygdaloid nucleus
Anterior nuclear group
Anterior olfactory nucleus
Basolateral amygdaloid nuclear complex
Bed nucleus of stria terminalis
Body of caudate nucleus
Central amygdaloid nucleus
Centromedian nucleus of thalamus
Cerebellar nuclear complex
Cerebellar vermis
Cerebrocerebellum
Claustrum of brain
Corticomedial nuclear complex
Cuneus cortex
Dentate gyrus of hippocampal formation
Dorsal tegmental nucleus
Epithalamus
Extrastriate cortex
Globus pallidus
Granular insular cortex
Gray matter of midbrain
Hippocampal field
Hypothalamus
Inferior frontal gyrus
Inferior olivary complex
Inferior temporal gyrus
Intralaminar nuclear group
Lateral amygdaloid nucleus
Lateral entorhinal cortex
Lateral geniculate body
Lateral nuclear group of thalamus
Lateral posterior nucleus of thalamus
Mammillary body
Medial dorsal nucleus of thalamus
Medial entorhinal cortex
Medial geniculate body
Medial zone of hypothalamus
Median tuberal portion
Midbrain nucleus
Midbrain tectum
Middle temporal gyrus
Nucleus accumbens
Nucleus of dorsal thalamus
Nucleus of medulla oblongata
Parabrachial nucleus
Perirhinal cortex
Piriform cortex
Pontine nuclear group
Pontine reticular formation
Pontine tegmentum
Posterior parahippocampal gyrus
Preoptic area
Pretectal region
Primary auditory cortex
Primary motor cortex
Primary somatosensory cortex
Primary visual cortex
Pulvinar nucleus
Putamen
Red nucleus
Retrosplenial region
Rostral ca3
Septal nuclear complex
Spinal cord
Subicular complex
Substantia innominata
Substantia nigra
Subthalamic nucleus
Superior parietal cortex
Superior temporal gyrus
Supraoptic nucleus
Temporal fusiform gyrus
Uncal ca1
Ventral anterior nucleus of thalamus
Developmental stage
42-year-old stage
29-year-old stage
50-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
Single Cell Portal
9,149 cells
Explore
Mus musculus
Mus musculus
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Endothelial cell of lymphatic vessel
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Related Links
Publication
CELLxGENE
9,110 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Podocyte
+5
Podocyte
Corpuscles of stannius
+5
Corpuscles of stannius
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Podocyte
Mesodermal cell
Endocrine cell
Epithelial cell of distal tubule
Multiciliated epithelial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Corpuscles of stannius
Distal tubule
Multicellular anatomical structure
Pronephric glomerulus
Pronephros
Proximal convoluted tubule
Developmental stage
Pharyngula:prim-15
Hatching:long-pec
Larval:protruding-mouth
Pharyngula:prim-25
Segmentation:26+ somites
Segmentation:14-19 somites
Hatching:pec-fin
Segmentation:20-25 somites
Pharyngula:high-pec
Pharyngula:prim-5
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
CELLxGENE
9,096 cells
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Club cell
+10
Club cell
Lung
Lung
Carnegie stage 19
+7
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Club cell
Lung secretory cell
Neuroendocrine cell
Pulmonary neuroendocrine cell
Basal cell
Respiratory tract epithelial cell
Pulmonary alveolar type 1 cell
Glandular secretory epithelial cell
Squamous epithelial cell
Epithelial cell of lung
Pulmonary alveolar type 2 cell
Tissue
Lung
Developmental stage
Carnegie stage 19
15th week post-fertilization stage
20th week post-fertilization stage
9th week post-fertilization stage
18th week post-fertilization stage
22nd week post-fertilization stage
Carnegie stage 16
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11265
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11266
CELLxGENE
9,070 cells
•
Yan et al., 2020
Cell Atlas of The Human Fovea and Peripheral Retina
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal cone cell
+1
Retinal cone cell
Fovea centralis
+1
Fovea centralis
69-year-old stage
+6
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Retinal cone cell
Retinal rod cell
Tissue
Fovea centralis
Peripheral region of retina
Developmental stage
69-year-old stage
65-year-old stage
53-year-old stage
74-year-old stage
64-year-old stage
60-year-old stage
78-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE148077
HumanCellAtlas:30dc3964-1135-4b56-b393-ce2dcbc6e379
BroadInstitute Single-Cell Portal:SCP839/cell-atlas-of-the-human-fovea-and-peripheral-retina
CELLxGENE
9,015 cells
•
Nowicki-Osuch et al., 2023
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Explore
h5ad
Homo sapiens
Homo sapiens
Iga plasma cell
+2
Iga plasma cell
Body of stomach
+7
Body of stomach
69-year-old stage
+24
69-year-old stage
Barrett esophagus
+3
Barrett esophagus
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Iga plasma cell
Igg plasma cell
Memory b cell
Tissue
Body of stomach
Cardia of stomach
Colon
Duodenum
Esophagogastric junction
Lower esophagus
Rectum
Submucosal esophageal gland
Developmental stage
69-year-old stage
34-year-old stage
42-year-old stage
43-year-old stage
53-year-old stage
54-year-old stage
68-year-old stage
48-year-old stage
29-year-old stage
56-year-old stage
55-year-old stage
50-year-old stage
51-year-old stage
57-year-old stage
74-year-old stage
80 year-old and over stage
58-year-old stage
67-year-old stage
77-year-old stage
45-year-old stage
62-year-old stage
41-year-old stage
63-year-old stage
83-year-old stage
27-year-old stage
Disease
Barrett esophagus
Normal
Gastric intestinal metaplasia
Gastritis
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001010074
Github:karolno/BE-GIM_Comparison
CELLxGENE
8,982 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
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
Endothelial cell of lymphatic vessel
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
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
GEO series:GSE195665
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
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