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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
221,425 cells
•
Xu et al., 2025
An integrated transcriptomic cell atlas of human endoderm-derived organoids
Explore
h5ad
Homo sapiens
Homo sapiens
Lung secretory cell
+8
Lung secretory cell
Nasopharynx
+4
Nasopharynx
Normal
Normal
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Lung secretory cell
Club cell
Pulmonary alveolar type 2 cell
Goblet cell
Pulmonary alveolar type 1 cell
Neuroendocrine cell
Ciliated cell
Basal cell
Stem cell
Tissue
Nasopharynx
Lung
Bronchus
Alveolar sac
Lung epithelium
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
Github:devsystemslab/HEOCA
Github:devsystemslab/sc2heoca
Github:devsystemslab/snapseed
Github:bioqxu/wilcoxauc
CELLxGENE
221,315 cells
•
Vázquez-García et al., 2022
Ovarian cancer mutational processes drive site-specific immune evasion
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
T cell
Abdominal wall
+18
Abdominal wall
78-year-old stage
+23
78-year-old stage
Malignant ovarian serous tumor
Malignant ovarian serous tumor
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Tissue
Abdominal wall
Paracolic gutter
Transverse colon
Parietal peritoneum
Caecum
Liver
Adnexa of uterus
Ascitic fluid
Right ovary
Peritoneum
Large intestine
Omentum
Urinary bladder
Left ovary
Abdomen
Intestine
Diaphragm
Fallopian tube
Lymph node
Developmental stage
78-year-old stage
80 year-old and over stage
61-year-old stage
57-year-old stage
70-year-old stage
45-year-old stage
41-year-old stage
59-year-old stage
55-year-old stage
58-year-old stage
75-year-old stage
50-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
77-year-old stage
69-year-old stage
76-year-old stage
63-year-old stage
60-year-old stage
56-year-old stage
46-year-old stage
71-year-old stage
47-year-old stage
Disease
Malignant ovarian serous tumor
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
dbGaP Study:phs002857
synapse.org:#!Synapse:syn25569736
GEO series:GSE180661
componcmsk.org
cbioportal.org
Github:shahcompbio/spectrum-tme
CELLxGENE
218,758 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+22
Fibroblast
Skin of body
+8
Skin of body
Carnegie stage 19
+13
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Pre-conventional dendritic cell
Kupffer cell
Common myeloid progenitor
Osteoclast
Hematopoietic multipotent progenitor cell
Mast cell
Langerhans cell
Granulocyte
Early lymphoid progenitor
Neutrophil
Common dendritic progenitor
Dendritic cell
Megakaryocyte
Hematopoietic stem cell
Plasmacytoid dendritic cell
Promonocyte
Megakaryocyte-erythroid progenitor cell
Granulocyte monocyte progenitor cell
Macrophage
Myelocyte
Monocyte
Promyelocyte
Tissue
Skin of body
Mesenteric lymph node
Liver
Gut wall
Bone marrow
Kidney
Spleen
Yolk sac
Thymus
Developmental stage
Carnegie stage 19
Carnegie stage 20
14th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 23
16th week post-fertilization stage
Carnegie stage 22
Carnegie stage 13
15th week post-fertilization stage
11th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
9th week post-fertilization stage
17th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
Github:Teichlab/Pan_fetal_immune
Human Cell Atlas Developmental:fetal-immune
Teichmann lab
UCSC Cell Browser:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
DOI:10.1016/j.stem.2018.12.011
BroadInstitute Single-Cell Portal:SCP1843
ArrayExpress BioStudies:E-MTAB-11341
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
CELLxGENE
216,611 cells
•
Domínguez Conde et al., 2022
Cross-tissue immune cell analysis reveals tissue-specific features in humans
Explore
h5ad
Homo sapiens
Homo sapiens
Effector memory cd4-positive, alpha-beta t cell
+15
Effector memory cd4-positive, alpha-beta t cell
Sigmoid colon
+16
Sigmoid colon
Sixth decade stage
+2
Sixth decade stage
Normal
Normal
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Effector memory cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Cd16-positive, cd56-dim natural killer cell, human
Alpha-beta t cell
Gamma-delta t cell
Regulatory t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Lymphocyte
Effector memory cd8-positive, alpha-beta t cell, terminally differentiated
Cd16-negative, cd56-bright natural killer cell, human
Group 3 innate lymphoid cell
Cd8-positive, alpha-beta memory t cell
Cd8-positive, alpha-beta memory t cell, cd45ro-positive
T follicular helper cell
Tissue
Sigmoid colon
Lung
Transverse colon
Caecum
Mesenteric lymph node
Liver
Lamina propria
Jejunal epithelium
Ileum
Blood
Bone marrow
Omentum
Spleen
Thymus
Skeletal muscle tissue
Duodenum
Thoracic lymph node
Developmental stage
Sixth decade stage
Eighth decade stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
10x 5' v1
Suspension type
Cell
Related Links
pan-immune.cells.ucsc.edu
celltypist.org
BroadInstitute Single-Cell Portal:SCP1845
HumanCellAtlas:04e4292c-f62f-4098-ae9b-fd69ae002a90
ArrayExpress BioStudies:E-MTAB-11536
CELLxGENE
216,507 cells
•
Lim et al., 2025
A non-canonical lymphoblast in refractory childhood T-cell leukaemia
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+14
Fibroblast
Bone marrow
Bone marrow
Pediatric stage
Pediatric stage
T-cell childhood acute lymphocytic leukemia
T-cell childhood acute lymphocytic leukemia
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Hematopoietic multipotent progenitor cell
Myeloid cell
Mast cell
Myeloid dendritic cell
Neutrophil
Malignant cell
Plasma cell
B cell
Plasmacytoid dendritic cell
Erythroid lineage cell
Natural killer cell
Monocyte
T cell
Megakaryocyte progenitor cell
Tissue
Bone marrow
Developmental stage
Pediatric stage
Disease
T-cell childhood acute lymphocytic leukemia
Sex
Female
Male
Technology
10x 5' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001009058
EGA dataset:EGAD00001015727
EGA dataset:EGAD00001015673
dbgap.ncbi.nlm.nih.gov
synapse.org:Synapse:syn54032669/wiki/627818
Github:BehjatiLab/TALL_refractory
EGA dataset:EGAD50000001128
CELLxGENE
215,278 cells
•
Zhang et al., 2023
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
Explore
h5ad
Mus musculus
Mus musculus
Astrocyte
+20
Astrocyte
Striatum
+10
Striatum
9-week-old stage
9-week-old stage
Normal
Normal
Male
Male
Merfish
Merfish
Organism
Mus musculus
Cell type
Astrocyte
Dopaminergic neuron
Neuroblast (sensu vertebrata)
Gabaergic neuron
Glycinergic neuron
Smooth muscle cell
Oligodendrocyte precursor cell
Oligodendrocyte
Dendritic cell
Bergmann glial cell
Pericyte
Lymphocyte
Ependymal cell
Glutamatergic neuron
Macrophage
Tanycyte
Monocyte
Vascular leptomeningeal cell
Microglial cell
Choroid plexus epithelial cell
Endothelial cell
Tissue
Striatum
Neocortex
Cortical subplate
Brain
Pallidum
Cerebellum
Hippocampal formation
White matter
Hindbrain
Thalamic complex
Ventricular system of brain
Developmental stage
9-week-old stage
Disease
Normal
Sex
Male
Technology
Merfish
Suspension type
Related Links
knowledge.brain-map.org
alleninstitute.github.io
alleninstitute.github.io
alleninstitute.github.io
alleninstitute.github.io
Github:ZhuangLab/MERlin
Github:ZhuangLab
Github:ZhuangLab/whole_mouse_brain_MERFISH_atlas_scripts_2023
CELLxGENE
215,278 cells
•
Zhang et al., 2023
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
Explore
h5ad
Mus musculus
Mus musculus
Astrocyte
+20
Astrocyte
Striatum
+10
Striatum
9-week-old stage
9-week-old stage
Normal
Normal
Male
Male
Merfish
Merfish
Organism
Mus musculus
Cell type
Astrocyte
Dopaminergic neuron
Neuroblast (sensu vertebrata)
Gabaergic neuron
Glycinergic neuron
Smooth muscle cell
Oligodendrocyte precursor cell
Oligodendrocyte
Dendritic cell
Bergmann glial cell
Pericyte
Lymphocyte
Ependymal cell
Glutamatergic neuron
Macrophage
Tanycyte
Monocyte
Vascular leptomeningeal cell
Microglial cell
Choroid plexus epithelial cell
Endothelial cell
Tissue
Striatum
Neocortex
Cortical subplate
Brain
Pallidum
Cerebellum
Hippocampal formation
White matter
Hindbrain
Thalamic complex
Ventricular system of brain
Developmental stage
9-week-old stage
Disease
Normal
Sex
Male
Technology
Merfish
Suspension type
Related Links
knowledge.brain-map.org
alleninstitute.github.io
alleninstitute.github.io
alleninstitute.github.io
alleninstitute.github.io
Github:ZhuangLab/MERlin
Github:ZhuangLab/whole_mouse_brain_MERFISH_atlas_scripts_2023
Github:ZhuangLab
CELLxGENE
215,067 cells
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Mus musculus
Mus musculus
Fibroblast
+37
Fibroblast
Forelimb
+1
Forelimb
Theiler stage 26
+8
Theiler stage 26
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Fibroblast
Primitive red blood cell
Innate lymphoid cell
Muscle fibroblast
Hair follicle melanocyte
Schwann cell
Common myeloid progenitor
Fibroblast of dermis
Mast cell
Vein endothelial cell
Smooth muscle cell
Peridermal cell
Basophil
Melanocyte
Chondroblast
Epithelial cell
Onychocyte
B cell
Skeletal muscle myoblast
Mesenchymal cell
Chondrocyte
Megakaryocyte
Pericyte
Muscle cell
Endothelial cell of lymphatic vessel
Tendon cell
Natural killer cell
Macrophage
Hypertrophic chondrocyte
Myelocyte
Schwann cell precursor
Erythrocyte
Osteoblast
Conventional dendritic cell
Monocyte
Basal cell
Myoblast
Endothelial cell of artery
Tissue
Forelimb
Hindlimb
Developmental stage
Theiler stage 26
Theiler stage 18
Theiler stage 24
Theiler stage 23
Theiler stage 20
Theiler stage 22
Theiler stage 16
Theiler stage 21
Theiler stage 19
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Human Cell Atlas Developmental:embryonic-limb
ArrayExpress BioStudies:E-MTAB-10514
ArrayExpress BioStudies:E-MTAB-10367
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
CELLxGENE
213,898 cells
•
Garcia-Alonso et al., 2022
Single-cell roadmap of human gonadal development
Explore
h5ad
Homo sapiens
Homo sapiens
Smooth muscle cell
+13
Smooth muscle cell
Gonad
Gonad
21st week post-fertilization stage
+13
21st week post-fertilization stage
Normal
Normal
Female
Female
10x 5' v2
+1
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Smooth muscle cell
Mural cell
Hematopoietic cell
Epithelial cell
Granulosa cell
Mesenchymal cell
Ovarian surface epithelial cell
Germ cell
Supporting cell
Neural cell
Erythrocyte
Interstitial cell of ovary
Mesothelial cell
Endothelial cell
Tissue
Gonad
Developmental stage
21st week post-fertilization stage
Carnegie stage 18
14th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 23
16th week post-fertilization stage
11th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 17
18th week post-fertilization stage
9th week post-fertilization stage
17th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
10x 5' v2
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10551
reproductivecellatlas.org
ventolab.org
ArrayExpress BioStudies:E-MTAB-11480
CELLxGENE
212,984 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+3
Fibroblast
Chorioretinal region
Chorioretinal region
62-year-old stage
+30
62-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Smooth muscle cell
Vascular associated smooth muscle cell
Pericyte
Tissue
Chorioretinal region
Developmental stage
62-year-old stage
27-year-old stage
72-year-old stage
53-year-old stage
21-year-old stage
81-year-old stage
Newborn stage (0-28 days)
82-year-old stage
17-year-old stage
86-year-old stage
30-year-old stage
10-year-old stage
58-year-old stage
90 year-old and over stage
50-year-old stage
64-year-old stage
68-year-old stage
77-year-old stage
11-year-old stage
69-year-old stage
32-year-old stage
63-year-old stage
60-year-old stage
25-year-old stage
46-year-old stage
43-year-old stage
65-year-old stage
71-year-old stage
34-year-old stage
16-year-old stage
47-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 5' v2
Suspension type
Nucleus
Related Links
celltype.info
CELLxGENE
210,107 cells
•
Vázquez-García et al., 2022
Ovarian cancer mutational processes drive site-specific immune evasion
Explore
h5ad
Homo sapiens
Homo sapiens
Fallopian tube secretory epithelial cell
Fallopian tube secretory epithelial cell
Abdominal wall
+18
Abdominal wall
78-year-old stage
+23
78-year-old stage
Malignant ovarian serous tumor
Malignant ovarian serous tumor
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fallopian tube secretory epithelial cell
Tissue
Abdominal wall
Paracolic gutter
Transverse colon
Parietal peritoneum
Caecum
Liver
Adnexa of uterus
Ascitic fluid
Right ovary
Peritoneum
Large intestine
Omentum
Urinary bladder
Left ovary
Abdomen
Intestine
Diaphragm
Fallopian tube
Lymph node
Developmental stage
78-year-old stage
80 year-old and over stage
61-year-old stage
57-year-old stage
70-year-old stage
45-year-old stage
41-year-old stage
59-year-old stage
55-year-old stage
58-year-old stage
75-year-old stage
50-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
77-year-old stage
69-year-old stage
76-year-old stage
63-year-old stage
60-year-old stage
56-year-old stage
46-year-old stage
71-year-old stage
47-year-old stage
Disease
Malignant ovarian serous tumor
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
dbGaP Study:phs002857
synapse.org:#!Synapse:syn25569736
GEO series:GSE180661
componcmsk.org
cbioportal.org
Github:shahcompbio/spectrum-tme
CELLxGENE
209,126 cells
•
Eraslan et al., 2022
Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+52
Fibroblast
Lingula of left lung
+7
Lingula of left lung
Third decade stage
+5
Third decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Professional antigen presenting cell
Slow muscle cell
Schwann cell
Luminal epithelial cell of mammary gland
Pulmonary alveolar epithelial cell
Endothelial cell of vascular tree
Keratinocyte
Elicited macrophage
Mast cell
Smooth muscle cell of prostate
Luminal cell of prostate epithelium
Cardiac endothelial cell
Epidermal cell
Alveolar macrophage
Melanocyte of skin
Contractile cell
Smooth muscle cell
Myeloid dendritic cell
Neutrophil
Interstitial cell of cajal
Bronchial epithelial cell
Epithelial cell of prostate
Cardiac muscle cell
Basal cell of epidermis
Dendritic cell
Basal epithelial cell of tracheobronchial tree
B cell
Subcutaneous adipocyte
Epidermal langerhans cell
Enteric smooth muscle cell
Glandular secretory epithelial cell
Sebaceous gland cell
Respiratory basal cell
Skin fibroblast
Adipocyte
Endothelial cell of lymphatic vessel
Macrophage
Neuroendocrine cell
Skeletal muscle fiber
Basal epithelial cell of prostatic duct
Skeletal muscle satellite cell
Skeletal muscle fibroblast
Basal-myoepithelial cell of mammary gland
Squamous epithelial cell
Mature nk t cell
Basal cell
Fibroblast of cardiac tissue
T cell
Neuron
Epithelial cell of sweat gland
Fast muscle cell
Fibroblast of breast
Tissue
Lingula of left lung
Skin of leg
Esophagus muscularis mucosa
Prostate gland
Mucosa
Gastrocnemius
Anterior wall of left ventricle
Breast
Developmental stage
Third decade stage
Sixth decade stage
Fourth decade stage
Eighth decade stage
Fifth decade stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
gtexportal.org
dbGaP Study:phs000424
HumanCellAtlas:31887183-a72c-4308-9eac-c6140313f39c
UCSC Cell Browser:cross-tissue-maps
BroadInstitute Single-Cell Portal:SCP1479/single-nucleus-cross-tissue-molecular-reference-maps
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