Molecular atlas of the adult mouse brain.(Dataset ID: STDS0000066)

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766
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6,767
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Spots: 34,103
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Genes: 23,371
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PMID: 32637622
Summary
Visualization
Data
Analysis results
Related
Sample
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette – that is sufficient to spatially annotate the adult brain. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.
Overall design:
We hybridized 75 coronal sections from one brain hemisphere of 3 adult mice with Spatial Transcriptomics and defined a molecular atlas using clustering algorithms.
Technology:
Spatial Transcriptomics
Platform:
Illumina NextSeq 500
Species:
Mus musculus
Tissues:
Brain
Development stage:
9 weeks
Sex:
Male
Submission date: 2020-03-30Update date: 2020-07-13
Sample number: 75
DOI: To be continue
Contributors
Cantin Ortiz,Jose Fernandez Navarro,Aleksandra Jurek,Antje Märtin,Joakim Lundeberg,Konstantinos Mele
Contact: dinos.meletis@ki.se
Accessions
GEO Series Accessions: GSE147747
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Cantin Ortiz,Jose Fernandez Navarro,Aleksandra Jurek,Antje Märtin,Joakim Lundeberg,Konstantinos Mele. Molecular atlas of the adult mouse brain.[DS/OL]. STOmicsDB, 2020[2020-03-30]. https://db.cngb.org/stomics/datasets/STDS0000066/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Ortiz, Cantin et al. “Molecular atlas of the adult mouse brain.” Science advances vol. 6,26 eabb3446. 26 Jun. 2020, doi:10.1126/sciadv.abb3446