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Cell
871
Nucleus
653
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Asap
43
Bgee
40
Cellxgene
2,045
Single cell portal
176
Sort
Most cells
Fewest cells
2304
datasets
CELLxGENE
74,812 cells
•
Bandesh et al., 2025
Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects
Explore
h5ad
Homo sapiens
Homo sapiens
Pancreatic a cell
Pancreatic a cell
Islet of langerhans
Islet of langerhans
54-year-old stage
+27
54-year-old stage
Type 2 diabetes mellitus
+2
Type 2 diabetes mellitus
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Pancreatic a cell
Tissue
Islet of langerhans
Developmental stage
54-year-old stage
35-year-old stage
62-year-old stage
26-year-old stage
53-year-old stage
21-year-old stage
61-year-old stage
57-year-old stage
49-year-old stage
42-year-old stage
52-year-old stage
48-year-old stage
40-year-old stage
38-year-old stage
45-year-old stage
59-year-old stage
30-year-old stage
55-year-old stage
58-year-old stage
50-year-old stage
51-year-old stage
66-year-old stage
32-year-old stage
63-year-old stage
60-year-old stage
25-year-old stage
37-year-old stage
34-year-old stage
Disease
Type 2 diabetes mellitus
Prediabetes syndrome
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
thejacksonlaboratory.shinyapps.io
Zenodo record:14656366
GEO series:GSE221156
CELLxGENE
74,626 cells
•
Kedlian et al., 2024
Human skeletal muscle aging atlas
Explore
h5ad
Homo sapiens
Homo sapiens
Type ii muscle cell
+2
Type ii muscle cell
Intercostal muscle
Intercostal muscle
Third decade stage
+5
Third decade stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Type ii muscle cell
Type i muscle cell
Muscle cell
Tissue
Intercostal muscle
Developmental stage
Third decade stage
Sixth decade stage
Fourth decade stage
Eighth decade stage
Young adult stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
muscleageingcellatlas.org
ArrayExpress BioStudies:E-MTAB-13874
CELLxGENE
73,409 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Neuron
Neuron
Lateral nuclear group of thalamus
+6
Lateral nuclear group of thalamus
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Neuron
Tissue
Lateral nuclear group of thalamus
Medial dorsal nucleus of thalamus
Lateral geniculate body
Ventral lateral nucleus of thalamus
Ventral thalamus
Dorsal thalamus
Thalamic complex
Developmental stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:dat-1je0mn3
submit.brainimagelibrary.org
CELLxGENE
73,347 cells
•
Yao et al., 2021
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Explore
h5ad
Mus musculus
Mus musculus
Cortical interneuron
+26
Cortical interneuron
Primary motor cortex
+19
Primary motor cortex
14-week-old stage
+8
14-week-old stage
Normal
Normal
Female
+1
Female
Smart-seq v4
Smart-seq v4
Cell
Cell
Organism
Mus musculus
Cell type
Cortical interneuron
L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex
L6b glutamatergic cortical neuron
Astrocyte
Lamp5 gabaergic interneuron
Sst chodl gabaergic interneuron
Corticothalamic-projecting glutamatergic cortical neuron
Vip gabaergic interneuron
L2/3-6 intratelencephalic projecting glutamatergic neuron
Oligodendrocyte
Pyramidal neuron
L6 corticothalamic-projecting glutamatergic cortical neuron
Pericyte
Hippocampal neuron
L5/6 near-projecting glutamatergic neuron of the primary motor cortex
Pvalb gabaergic interneuron
Meis2 expressing cortical gabaergic cell
L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex
Glutamatergic neuron
Cajal-retzius cell
Sncg gabaergic interneuron
Central nervous system macrophage
Sst gabaergic interneuron
L5 extratelencephalic projecting glutamatergic cortical neuron
L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex
Endothelial cell
Vascular leptomeningeal cell (mmus)
Tissue
Primary motor cortex
Medial orbital frontal cortex
Primary visual cortex
Primary somatosensory cortex
Posterior parietal association areas
Retrosplenial region
Temporal cortex
Lateral entorhinal cortex
Auditory cortex
Agranular insular cortex
Gustatory cortex
Hippocampal formation
Anterior cingulate cortex
Medial entorhinal cortex
Prefrontal cortex
Secondary somatosensory cortex
Visual cortex
Subicular complex
Frontal cortex
Claustrum of brain
Developmental stage
14-week-old stage
12-week-old stage
11-week-old stage
8-week-old stage
7-week-old stage
9-week-old stage
13-week-old stage
10-week-old stage
15-week-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq v4
Suspension type
Cell
Related Links
Allen Brain Map Atlases:rnaseq/mouse-whole-cortex-and-hippocampus-10x
GEO series:GSE185862
NeMo archive:dat-jb2f34y
Allen Brain Map Atlases:rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq
CELLxGENE
73,295 cells
•
Andrews et al., 2021
Single‐Cell, Single‐Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Periportal region hepatocyte
+11
Periportal region hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Young adult stage
+1
Young adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Periportal region hepatocyte
Kupffer cell
Inflammatory macrophage
Cholangiocyte
B cell
Midzonal region hepatocyte
Blood vessel endothelial cell
Centrilobular region hepatocyte
Erythroid lineage cell
Natural killer cell
Hepatic stellate cell
Endothelial cell of pericentral hepatic sinusoid
Tissue
Caudate lobe of liver
Developmental stage
Young adult stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Nucleus
Related Links
Github:tallulandrews/Liver_sc_sn_paper_scripts
GEO series:GSE185477
protocols.io:human-liver-caudate-lobe-dissociation-for-scrna-se-q26g77j1gwz1/v2
macparlandlab.shinyapps.io
HumanCellAtlas:8a666b76-daaf-4b1f-9414-e4807a1d1e8b
CELLxGENE
73,195 cells
•
The Tabula Sapiens Consortium* et al., 2022
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of vascular tree
+10
Endothelial cell of vascular tree
Vasculature
+68
Vasculature
74-year-old stage
+16
74-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of vascular tree
Endothelial cell of arteriole
Cardiac endothelial cell
Vein endothelial cell
Colon endothelial cell
Capillary endothelial cell
Endothelial cell of venule
Endothelial cell of lymphatic vessel
Retinal blood vessel endothelial cell
Endothelial cell
Endothelial cell of artery
Tissue
Vasculature
Skin of body
Trachea
Cardiac ventricle
Chorioretinal region
Myometrium
Brown adipose tissue
Left coronary artery
Lacrimal gland
Stomach
Ascending colon
Endometrium
Sigmoid colon
Lung
Crista ampullaris
Bladder organ
Aorta
Subcutaneous adipose tissue
Mesenteric lymph node
Liver
Mucosa of stomach
Conjunctiva
Exocrine pancreas
Ileum
Stomach smooth muscle
Right cardiac atrium
Muscle of abdomen
Cornea
Inferior vena cava
Right ovary
Prostate gland
Skin of chest
Abdominal aorta
Large intestine
Bone marrow
Sclera
Cardiac atrium
Posterior part of tongue
Kidney
Sublingual gland
Adipose tissue
Eyelid
Ovary
Spleen
Anterior part of tongue
Thoracic aorta
Uterus
Muscle of pelvic diaphragm
Small intestine
Thymus
Left ovary
Buccal mucosa
Posterior segment of eyeball
Heart
Skin of abdomen
Jejunum
Heart right ventricle
Anterior segment of eyeball
Coronary artery
Duodenum
Parotid gland
Mammary gland
Submandibular gland
Testis
Inguinal lymph node
Lymph node
Endocrine pancreas
Eye
Utricle of membranous labyrinth
Developmental stage
74-year-old stage
26-year-old stage
61-year-old stage
57-year-old stage
36-year-old stage
40-year-old stage
38-year-old stage
45-year-old stage
59-year-old stage
55-year-old stage
33-year-old stage
69-year-old stage
60-year-old stage
56-year-old stage
37-year-old stage
46-year-old stage
67-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Smart-seq3
10x 5' v2
Smart-seq2
Suspension type
Cell
Related Links
CZ BioHub Portal:tabula-sapiens-portal
UCSC Cell Browser:tabula-sapiens
DOI:10.1101/2024.12.03.626516
AWS Open Data:tabula-sapiens
HumanCellAtlas:10201832-7c73-4033-9b65-3ef13d81656a
UCSC Genome Browser:hgTrackUi?hgsid=1437536541_FfasmBrAlAiA7oFphu1csVv0KHgc&db=hg38&c=chrX&g=tabulaSapiens
CELLxGENE
73,047 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
Myeloid cell
+5
Myeloid cell
Adrenal gland
+7
Adrenal gland
62-year-old stage
+24
62-year-old stage
Normal
+2
Normal
Female
+1
Female
10x 3' transcription profiling
+2
10x 3' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Myeloid cell
Mast cell
Plasma cell
B cell
Natural killer cell
T cell
Tissue
Adrenal gland
Lung
Pleural effusion
Liver
Brain
Bone spine
Axilla
Lymph node
Developmental stage
62-year-old stage
78-year-old stage
73-year-old stage
74-year-old stage
72-year-old stage
85-year-old stage
81-year-old stage
57-year-old stage
82-year-old stage
70-year-old stage
55-year-old stage
75-year-old stage
79-year-old stage
64-year-old stage
68-year-old stage
77-year-old stage
69-year-old stage
76-year-old stage
80-year-old stage
84-year-old stage
67-year-old stage
65-year-old stage
71-year-old stage
44-year-old stage
47-year-old stage
Disease
Normal
Lung adenocarcinoma
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
CELLxGENE
72,788 cells
•
Li et al., 2023
Integrated multi-omics single cell atlas of the human retina
Explore
h5ad
Homo sapiens
Homo sapiens
Offx cell
+12
Offx cell
Chorioretinal region
+4
Chorioretinal region
54-year-old stage
+15
54-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Offx cell
Invaginating midget bipolar cell
Retinal bipolar neuron
Diffuse bipolar 3b cell
Diffuse bipolar 4 cell
Diffuse bipolar 3a cell
Diffuse bipolar 6 cell
Giant bipolar cell
On-blue cone bipolar cell
Rod bipolar cell
Flat midget bipolar cell
Diffuse bipolar 1 cell
Diffuse bipolar 2 cell
Tissue
Chorioretinal region
Peripheral region of retina
Fovea centralis
Retinal neural layer
Macula lutea proper
Developmental stage
54-year-old stage
Adult stage
78-year-old stage
74-year-old stage
53-year-old stage
82-year-old stage
42-year-old stage
86-year-old stage
89-year-old stage
64-year-old stage
68-year-old stage
69-year-old stage
60-year-old stage
80-year-old stage
65-year-old stage
71-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:RCHENLAB/HRCA_reproducibility
CELLxGENE
72,695 cells
•
Nieto et al., 2025
Decoding the immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell, human
+7
Dendritic cell, human
Cerebrospinal fluid
Cerebrospinal fluid
54-year-old stage
+14
54-year-old stage
Brain cancer
+3
Brain cancer
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Dendritic cell, human
Stromal cell
B cell
Cd8-positive, alpha-beta t cell
Natural killer cell
Macrophage
Monocyte
Cd4-positive, alpha-beta t cell
Tissue
Cerebrospinal fluid
Developmental stage
54-year-old stage
73-year-old stage
61-year-old stage
70-year-old stage
40-year-old stage
45-year-old stage
55-year-old stage
58-year-old stage
69-year-old stage
63-year-old stage
60-year-old stage
56-year-old stage
67-year-old stage
71-year-old stage
34-year-old stage
Disease
Brain cancer
Lymphoma
Glioblastoma
Inflammatory disease
Sex
Female
Male
Technology
10x 5' v2
Suspension type
Cell
Related Links
GEO series:GSE286518
Github:Single-Cell-Genomics-Group-CNAG-CRG/CSF
CELLxGENE
72,356 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Enteroendocrine cell
+10
Enteroendocrine cell
Ileum lamina propria
+9
Ileum lamina propria
9-year-old stage
+20
9-year-old stage
Crohn disease
+1
Crohn disease
Female
+1
Female
10x 5' transcription profiling
+4
10x 5' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Enteroendocrine cell
Transit amplifying cell
Enterocyte
Tuft cell of small intestine
Paneth cell
Intestine goblet cell
Mucous neck cell of gastric gland
Foveolar cell of stomach
Best4+ enterocyte
Intestinal crypt stem cell
M cell of gut
Tissue
Ileum lamina propria
Ileal epithelium
Mesenteric lymph node
Ileum
Small intestine
Duodenal epithelium
Jejunum
Duodenum
Epithelium of small intestine
Lamina propria of small intestine
Developmental stage
9-year-old stage
Third decade stage
13-year-old stage
Sixth decade stage
4-year-old stage
52-year-old stage
6-year-old stage
12-year-old stage
45-year-old stage
Eighth decade stage
10-year-old stage
14-year-old stage
50-year-old stage
11-year-old stage
Fifth decade stage
31-year-old stage
87-year-old stage
60-year-old stage
Prime adult stage
67-year-old stage
Seventh decade stage
Disease
Crohn disease
Normal
Sex
Female
Male
Technology
10x 5' transcription profiling
10x 3' v1
10x 5' v2
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
72,335 cells
•
Efthymiou et al., 2025
Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles
Explore
h5ad
Homo sapiens
Homo sapiens
Fibro/adipogenic progenitor cell
+13
Fibro/adipogenic progenitor cell
Subcutaneous abdominal adipose tissue
+1
Subcutaneous abdominal adipose tissue
54-year-old stage
+13
54-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibro/adipogenic progenitor cell
Schwann cell
Myeloid cell
Mast cell
Smooth muscle cell
Hematopoietic cell
Pericyte
Lymphocyte
Adipocyte
Endothelial cell of lymphatic vessel
Macrophage
Neuron associated cell
Mesothelial cell
Endothelial cell
Tissue
Subcutaneous abdominal adipose tissue
Visceral abdominal adipose tissue
Developmental stage
54-year-old stage
35-year-old stage
62-year-old stage
27-year-old stage
26-year-old stage
53-year-old stage
21-year-old stage
41-year-old stage
18-year-old stage
51-year-old stage
66-year-old stage
28-year-old stage
37-year-old stage
47-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Single Cell Portal
72,128 cells
Explore
Homo sapiens
Homo sapiens
Endothelial cell of vascular tree
+21
Endothelial cell of vascular tree
Cervical cancer
Cervical cancer
10x 3' v3
10x 3' v3
Organism
Homo sapiens
Cell type
Endothelial cell of vascular tree
Keratinocyte
Neural progenitor cell
Mesenchymal stem cell
Epithelial cell
Cd141-positive myeloid dendritic cell
Malignant cell
B cell
Gamma-delta t cell
Regulatory t cell
Pericyte
Myofibroblast cell
Plasmacytoid dendritic cell
Cd8-positive, alpha-beta t cell
Endothelial cell of lymphatic vessel
Granulocyte monocyte progenitor cell
Natural killer cell
Macrophage
Mesenchymal stem cell of adipose tissue
Basal cell
Naive b cell
Endothelial cell
Tissue
Developmental stage
Disease
Cervical cancer
Sex
Technology
10x 3' v3
Suspension type
1
2
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46
47
48
49
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