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890
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655
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Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
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2328
datasets
CELLxGENE
218,758 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Common myeloid progenitor
+22
Common myeloid progenitor
Thymus
+8
Thymus
9th week post-fertilization stage
+13
9th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Common myeloid progenitor
Kupffer cell
Pre-conventional dendritic cell
Promonocyte
Osteoclast
Macrophage
Granulocyte monocyte progenitor cell
Promyelocyte
Mast cell
Megakaryocyte-erythroid progenitor cell
Neutrophil
Monocyte
Megakaryocyte
Granulocyte
Early lymphoid progenitor
Fibroblast
Hematopoietic stem cell
Dendritic cell
Plasmacytoid dendritic cell
Common dendritic progenitor
Myelocyte
Hematopoietic multipotent progenitor cell
Langerhans cell
Tissue
Thymus
Mesenteric lymph node
Liver
Spleen
Kidney
Bone marrow
Gut wall
Yolk sac
Skin of body
Developmental stage
9th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 22
11th week post-fertilization stage
17th week post-fertilization stage
15th week post-fertilization stage
Carnegie stage 19
Carnegie stage 13
14th week post-fertilization stage
16th week post-fertilization stage
Carnegie stage 23
Carnegie stage 20
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
Teichmann lab
UCSC Cell Browser:fetal-immune
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
BroadInstitute Single-Cell Portal:SCP1843
Human Cell Atlas Developmental:fetal-immune
ArrayExpress BioStudies:E-MTAB-11343
ArrayExpress BioStudies:E-MTAB-11341
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
Cd8-positive, alpha-beta memory t cell, cd45ro-positive
+15
Cd8-positive, alpha-beta memory t cell, cd45ro-positive
Blood
+16
Blood
Eighth decade stage
+2
Eighth decade stage
Normal
Normal
Female
+1
Female
10x 5' v2
+2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Cd8-positive, alpha-beta memory t cell, cd45ro-positive
Lymphocyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Effector memory cd4-positive, alpha-beta t cell
Cd4-positive helper t cell
Cd16-negative, cd56-bright natural killer cell, human
Cd8-positive, alpha-beta memory t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Group 3 innate lymphoid cell
Alpha-beta t cell
Regulatory t cell
Effector memory cd8-positive, alpha-beta t cell, terminally differentiated
T follicular helper cell
Gamma-delta t cell
Cd16-positive, cd56-dim natural killer cell, human
Tissue
Blood
Ileum
Thymus
Mesenteric lymph node
Liver
Spleen
Skeletal muscle tissue
Caecum
Lung
Lamina propria
Transverse colon
Omentum
Sigmoid colon
Duodenum
Bone marrow
Jejunal epithelium
Thoracic lymph node
Developmental stage
Eighth decade stage
Seventh decade stage
Sixth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
10x 3' v3
Suspension type
Cell
Related Links
pan-immune.cells.ucsc.edu
celltypist.org
BroadInstitute Single-Cell Portal:SCP1845
ArrayExpress BioStudies:E-MTAB-11536
HumanCellAtlas:04e4292c-f62f-4098-ae9b-fd69ae002a90
CELLxGENE
216,507 cells
•
Lim et al., 2025
A non-canonical lymphoblast in refractory childhood T-cell leukaemia
Explore
h5ad
Homo sapiens
Homo sapiens
Megakaryocyte progenitor cell
+14
Megakaryocyte progenitor cell
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
Megakaryocyte progenitor cell
Mast cell
Erythroid lineage cell
Neutrophil
Monocyte
Myeloid dendritic cell
Fibroblast
Malignant cell
B cell
Plasma cell
T cell
Plasmacytoid dendritic cell
Natural killer cell
Hematopoietic multipotent progenitor cell
Myeloid 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:EGAD50000001128
EGA dataset:EGAD00001015727
EGA dataset:EGAD00001015673
dbgap.ncbi.nlm.nih.gov
Github:BehjatiLab/TALL_refractory
synapse.org:Synapse:syn54032669/wiki/627818
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
Glutamatergic neuron
+20
Glutamatergic neuron
Hippocampal formation
+10
Hippocampal formation
9-week-old stage
9-week-old stage
Normal
Normal
Male
Male
Merfish
Merfish
Organism
Mus musculus
Cell type
Glutamatergic neuron
Vascular leptomeningeal cell
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Gabaergic neuron
Lymphocyte
Macrophage
Neuroblast (sensu vertebrata)
Glycinergic neuron
Bergmann glial cell
Monocyte
Dopaminergic neuron
Microglial cell
Tanycyte
Ependymal cell
Pericyte
Endothelial cell
Dendritic cell
Smooth muscle cell
Choroid plexus epithelial cell
Tissue
Hippocampal formation
Cortical subplate
Cerebellum
Thalamic complex
Pallidum
Brain
Striatum
Neocortex
White matter
Ventricular system of brain
Hindbrain
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
215,278 cells
•
Zhang et al., 2023
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
+20
Glutamatergic neuron
Hippocampal formation
+10
Hippocampal formation
9-week-old stage
9-week-old stage
Normal
Normal
Male
Male
Merfish
Merfish
Organism
Mus musculus
Cell type
Glutamatergic neuron
Vascular leptomeningeal cell
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Gabaergic neuron
Lymphocyte
Macrophage
Neuroblast (sensu vertebrata)
Glycinergic neuron
Bergmann glial cell
Monocyte
Dopaminergic neuron
Microglial cell
Tanycyte
Ependymal cell
Pericyte
Endothelial cell
Dendritic cell
Smooth muscle cell
Choroid plexus epithelial cell
Tissue
Hippocampal formation
Cortical subplate
Cerebellum
Thalamic complex
Pallidum
Brain
Striatum
Neocortex
White matter
Ventricular system of brain
Hindbrain
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
Osteoblast
+37
Osteoblast
Hindlimb
+1
Hindlimb
Theiler stage 23
+8
Theiler stage 23
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Osteoblast
Skeletal muscle myoblast
Common myeloid progenitor
Schwann cell
Peridermal cell
Innate lymphoid cell
Endothelial cell of lymphatic vessel
Muscle cell
Macrophage
Mast cell
Basal cell
Epithelial cell
Onychocyte
Monocyte
Tendon cell
Megakaryocyte
Myoblast
Schwann cell precursor
Vein endothelial cell
Primitive red blood cell
Conventional dendritic cell
Fibroblast
Pericyte
Mesenchymal cell
B cell
Erythrocyte
Fibroblast of dermis
Myelocyte
Hypertrophic chondrocyte
Muscle fibroblast
Chondroblast
Smooth muscle cell
Basophil
Natural killer cell
Chondrocyte
Endothelial cell of artery
Melanocyte
Hair follicle melanocyte
Tissue
Hindlimb
Forelimb
Developmental stage
Theiler stage 23
Theiler stage 24
Theiler stage 21
Theiler stage 16
Theiler stage 26
Theiler stage 18
Theiler stage 20
Theiler stage 19
Theiler stage 22
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-8813
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-10367
CELLxGENE
213,898 cells
•
Garcia-Alonso et al., 2022
Single-cell roadmap of human gonadal development
Explore
h5ad
Homo sapiens
Homo sapiens
Germ cell
+13
Germ cell
Gonad
Gonad
9th week post-fertilization stage
+13
9th week post-fertilization stage
Normal
Normal
Female
Female
10x 5' v2
+1
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Germ cell
Mural cell
Supporting cell
Mesothelial cell
Epithelial cell
Hematopoietic cell
Endothelial cell
Ovarian surface epithelial cell
Interstitial cell of ovary
Mesenchymal cell
Erythrocyte
Granulosa cell
Smooth muscle cell
Neural cell
Tissue
Gonad
Developmental stage
9th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
10th week post-fertilization stage
11th week post-fertilization stage
21st week post-fertilization stage
17th week post-fertilization stage
14th week post-fertilization stage
16th week post-fertilization stage
18th week post-fertilization stage
Carnegie stage 23
Carnegie stage 17
Carnegie stage 21
Carnegie stage 18
Disease
Normal
Sex
Female
Technology
10x 5' v2
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10551
ArrayExpress BioStudies:E-MTAB-11480
reproductivecellatlas.org
ventolab.org
CELLxGENE
212,984 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Vascular associated smooth muscle cell
+3
Vascular associated smooth muscle cell
Chorioretinal region
Chorioretinal region
82-year-old stage
+30
82-year-old stage
Normal
Normal
Female
+1
Female
10x 5' v2
+1
10x 5' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Smooth muscle cell
Tissue
Chorioretinal region
Developmental stage
82-year-old stage
16-year-old stage
77-year-old stage
21-year-old stage
32-year-old stage
50-year-old stage
86-year-old stage
62-year-old stage
46-year-old stage
60-year-old stage
64-year-old stage
25-year-old stage
65-year-old stage
27-year-old stage
71-year-old stage
63-year-old stage
47-year-old stage
58-year-old stage
68-year-old stage
34-year-old stage
53-year-old stage
10-year-old stage
17-year-old stage
72-year-old stage
30-year-old stage
Newborn stage (0-28 days)
69-year-old stage
43-year-old stage
90 year-old and over stage
81-year-old stage
11-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v3
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
66-year-old stage
+23
66-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
Liver
Adnexa of uterus
Right ovary
Caecum
Fallopian tube
Transverse colon
Urinary bladder
Omentum
Diaphragm
Parietal peritoneum
Peritoneum
Paracolic gutter
Ascitic fluid
Abdomen
Intestine
Left ovary
Large intestine
Lymph node
Developmental stage
66-year-old stage
70-year-old stage
77-year-old stage
50-year-old stage
57-year-old stage
76-year-old stage
46-year-old stage
60-year-old stage
80 year-old and over stage
64-year-old stage
45-year-old stage
75-year-old stage
71-year-old stage
78-year-old stage
63-year-old stage
59-year-old stage
47-year-old stage
56-year-old stage
58-year-old stage
68-year-old stage
61-year-old stage
69-year-old stage
41-year-old stage
55-year-old stage
Disease
Malignant ovarian serous tumor
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
synapse.org:#!Synapse:syn25569736
GEO series:GSE180661
componcmsk.org
cbioportal.org
Github:shahcompbio/spectrum-tme
dbGaP Study:phs002857
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
Subcutaneous adipocyte
+52
Subcutaneous adipocyte
Breast
+7
Breast
Fourth decade stage
+5
Fourth decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Subcutaneous adipocyte
Slow muscle cell
Luminal cell of prostate epithelium
Schwann cell
Skin fibroblast
Skeletal muscle fibroblast
Enteric smooth muscle cell
Contractile cell
Cardiac endothelial cell
Cardiac muscle cell
Endothelial cell of lymphatic vessel
Macrophage
Alveolar macrophage
Melanocyte of skin
Glandular secretory epithelial cell
Interstitial cell of cajal
Mast cell
Basal epithelial cell of prostatic duct
Basal cell
Endothelial cell of vascular tree
Sebaceous gland cell
Fibroblast of breast
Adipocyte
Neutrophil
Basal epithelial cell of tracheobronchial tree
Epithelial cell of sweat gland
Myeloid dendritic cell
Skeletal muscle fiber
Basal cell of epidermis
Luminal epithelial cell of mammary gland
Smooth muscle cell of prostate
Fibroblast
Epithelial cell of prostate
Skeletal muscle satellite cell
B cell
Epidermal cell
Squamous epithelial cell
Dendritic cell
Pulmonary alveolar epithelial cell
Epidermal langerhans cell
Fibroblast of cardiac tissue
Mature nk t cell
T cell
Neuroendocrine cell
Basal-myoepithelial cell of mammary gland
Smooth muscle cell
Respiratory basal cell
Neuron
Keratinocyte
Professional antigen presenting cell
Fast muscle cell
Elicited macrophage
Bronchial epithelial cell
Tissue
Breast
Gastrocnemius
Anterior wall of left ventricle
Esophagus muscularis mucosa
Prostate gland
Lingula of left lung
Skin of leg
Mucosa
Developmental stage
Fourth decade stage
Eighth decade stage
Fifth decade stage
Seventh decade stage
Third decade stage
Sixth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
gtexportal.org
HumanCellAtlas:31887183-a72c-4308-9eac-c6140313f39c
UCSC Cell Browser:cross-tissue-maps
dbGaP Study:phs000424
BroadInstitute Single-Cell Portal:SCP1479/single-nucleus-cross-tissue-molecular-reference-maps
CELLxGENE
208,390 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Breast
Breast
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Breast
Developmental stage
Prime adult stage
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
CELLxGENE
207,952 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Cd1c-positive myeloid dendritic cell
+27
Cd1c-positive myeloid dendritic cell
Blood
Blood
82-year-old stage
+6
82-year-old stage
Open-angle glaucoma
+1
Open-angle glaucoma
Female
+1
Female
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Cd1c-positive myeloid dendritic cell
Activated cd8-positive, alpha-beta t cell
Naive b cell
Innate lymphoid cell
Cd4-positive, alpha-beta memory t cell
Platelet
Mature b cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Cd141-positive myeloid dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Erythroid lineage cell
Plasmablast
Cd14-positive, cd16-negative classical monocyte
Cd8-positive, alpha-beta memory t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Hematopoietic precursor cell
Effector cd4-positive, alpha-beta t cell
Cd4-positive, alpha-beta cytotoxic t cell
Activated cd4-positive, alpha-beta t cell
Dendritic cell
Regulatory t cell
Memory b cell
Plasmacytoid dendritic cell
Cd4-negative, cd8-negative, alpha-beta intraepithelial t cell
Cd14-low, cd16-positive monocyte
Natural killer cell
Gamma-delta t cell
Tissue
Blood
Developmental stage
82-year-old stage
77-year-old stage
74-year-old stage
67-year-old stage
63-year-old stage
58-year-old stage
69-year-old stage
Disease
Open-angle glaucoma
Normal
Sex
Female
Male
Technology
10x 5' v2
Suspension type
Cell
Related Links
Github:mcrewcow/PBMC_Glaucoma_human
GEO series:GSE268936
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