The molecular cytoarchitecture of the adult mouse brain

Langlieb, Jonah, Sachdev, Nina S, Balderrama, Karol S, Nadaf, Naeem M, Raj, Mukund, Murray, Evan, Webber, James T, Vanderburg, Charles, Gazestani, Vahid, Tward, Daniel, Mezias, Chris, Li, Xu, Flowers, Katelyn, Cable, Dylan M, Norton, Tabitha, Mitra, Partha, Chen, Fei, Macosko, Evan Z (December 2023) The molecular cytoarchitecture of the adult mouse brain. Nature, 624 (7991). pp. 333-342. ISSN 0028-0836

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Abstract

The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types and their positions within individual anatomical structures remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq1,2-a recently developed spatial transcriptomics method with near-cellular resolution-across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signalling, elucidated region-specific specializations in activity-regulated gene expression and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource ( www.BrainCellData.org ), should find diverse applications across neuroscience, including the construction of new genetic tools and the prioritization of specific cell types and circuits in the study of brain diseases.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > animal organs, tissues, organelles, cell types and functions > organs types and functions > brain organs, tissues, organelles, cell types and functions > tissues types and functions > suprachiasmatic nucleus > hypothalamus organs, tissues, organelles, cell types and functions > tissues types and functions > hypothalamus organism description > animal > mammal organism description > animal > mammal > rodent > mouse neurobiology neurobiology > neuroscience organs, tissues, organelles, cell types and functions > organs types and functions organs, tissues, organelles, cell types and functions organism description > animal > mammal > rodent neurobiology > neuroscience > systems neuroscience organs, tissues, organelles, cell types and functions > tissues types and functions bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:	Li, Xu Mitra, Partha P. Mezias, Christopher
Communities:	CSHL labs > Mitra lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	December 2023
Date Deposited:	20 Dec 2023 19:30
Last Modified:	10 Jan 2024 20:07
PMCID:	PMC10719111
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41342

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