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Organism
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Cell Type
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Tissue
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Developmental Stage
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Disease
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Sex
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Technology
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Suspension Type
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Cell
896
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
ASAP
1,000 cells
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell
+9
Endothelial cell
Retina
Retina
Organism
Mus musculus
Cell type
Endothelial cell
Retinal ganglion cell
Rod bipolar cell
Cone retinal bipolar cell
Microglial cell
Retinal cone cell
Retinal rod cell
Glial cell
Amacrine cell
Pericyte
Tissue
Retina
Developmental stage
Disease
Sex
Technology
Suspension type
CELLxGENE
959 cells
•
Anderson-Crannage et al., 2023
Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin
Explore
h5ad
Mus musculus
Mus musculus
Neutrophil
+8
Neutrophil
Autopod skin
Autopod skin
2-week-old stage
2-week-old stage
Epidermolysis bullosa
+1
Epidermolysis bullosa
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Neutrophil
Endothelial cell
Schwann cell
Fibroblast of lymphatic vessel
Innate lymphoid cell
Pericyte
Professional antigen presenting cell
Fibroblast
Chondrocyte
Tissue
Autopod skin
Developmental stage
2-week-old stage
Disease
Epidermolysis bullosa
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE222250
CELLxGENE
955 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Regular atrial cardiac myocyte
Regular atrial cardiac myocyte
Atrioventricular node
Atrioventricular node
Fifth decade stage
+1
Fifth decade stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Regular atrial cardiac myocyte
Tissue
Atrioventricular node
Developmental stage
Fifth decade stage
Eighth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
CELLxGENE
935 cells
•
Moorman et al., 2025
Author Correction: Progressive plasticity during colorectal cancer metastasis
Explore
h5ad
Homo sapiens
Homo sapiens
Malignant cell
Malignant cell
Liver
+2
Liver
44-year-old stage
44-year-old stage
Colorectal cancer
Colorectal cancer
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Malignant cell
Tissue
Liver
Rectum
Chest wall
Developmental stage
44-year-old stage
Disease
Colorectal cancer
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:dpeerlab/progressive-plasticity-crc-metastasis.git
CELLxGENE
906 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Epithelial cell
+5
Epithelial cell
Aorta
Aorta
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Epithelial cell
Macrophage
Aortic endothelial cell
Professional antigen presenting cell
Circulating fibrocyte
Fibroblast of cardiac tissue
Tissue
Aorta
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
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
Single Cell Portal
894 cells
Explore
Mus musculus
Mus musculus
Neuron
Neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
CELLxGENE
893 cells
•
Fujimoto et al., 2020
Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Explore
h5ad
Mus musculus
Mus musculus
Lymphatic endothelial cell of medulla ceiling
+3
Lymphatic endothelial cell of medulla ceiling
Inguinal lymph node
Inguinal lymph node
2-month-old stage
2-month-old stage
Normal
Normal
Female
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Lymphatic endothelial cell of medulla ceiling
Lymph node lymphatic vessel endothelial cell
Lymphatic endothelial cell of subcapsular sinus ceiling
Lymphatic endothelial cell of subcapsular sinus floor
Tissue
Inguinal lymph node
Developmental stage
2-month-old stage
Disease
Normal
Sex
Female
Technology
Smart-seq2
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-8414
Single Cell Portal
879 cells
Explore
Mus musculus
Mus musculus
Granule cell
+1
Granule cell
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Granule cell
Purkinje cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
CELLxGENE
873 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Neuroplacodal cell
Neuroplacodal cell
Medulla oblongata
+5
Medulla oblongata
Carnegie stage 20
+4
Carnegie stage 20
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neuroplacodal cell
Tissue
Medulla oblongata
Hindbrain
Midbrain
Cerebellum
Forebrain
Head
Developmental stage
Carnegie stage 20
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 16
Carnegie stage 15
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001006049
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
CELLxGENE
871 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Neural crest cell
Neural crest cell
Striatum
+14
Striatum
13th week post-fertilization stage
+8
13th week post-fertilization stage
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neural crest cell
Tissue
Striatum
Medulla oblongata
Hindbrain
Cortex
Midbrain
Lower layers of the cortex
Metencephalon
Basal forebrain
Cerebellum
Hypothalamus
Cerebellar peduncular complex
Pons
Cerebral subcortex
Forebrain
Head
Developmental stage
13th week post-fertilization stage
14th week post-fertilization stage
15th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 16
Carnegie stage 15
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
EGA dataset:EGAD00001006049
Single Cell Portal
844 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+3
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Obsolete excitatory neuron
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD699) (section 368)
CELLxGENE
843 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+6
Neutrophil
Thymus
Thymus
13th week post-fertilization stage
+11
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+3
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Erythrocyte
Myelocyte
Promonocyte
Common myeloid progenitor
Granulocyte monocyte progenitor cell
Monocyte
Tissue
Thymus
Developmental stage
13th week post-fertilization stage
3-month-old stage
14th week post-fertilization stage
15th week post-fertilization stage
20th week post-fertilization stage
17th week post-fertilization stage
12th week post-fertilization stage
6-month-old stage
18th week post-fertilization stage
Newborn stage (0-28 days)
24th week post-fertilization stage
14-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Bioimage Archive:S-BIAD1257
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