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    A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

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    Author
    Yao, Zizhen
    Liu, Hanqing
    Xie, Fangming
    Fischer, Stephan
    Adkins, Ricky S
    Aldridge, Andrew I
    Ament, Seth A
    Bartlett, Anna
    Behrens, M Margarita
    Van den Berge, Koen
    Bertagnolli, Darren
    de Bézieux, Hector Roux
    Biancalani, Tommaso
    Booeshaghi, A Sina
    Bravo, Héctor Corrada
    Casper, Tamara
    Colantuoni, Carlo
    Crabtree, Jonathan
    Creasy, Heather
    Crichton, Kirsten
    Crow, Megan
    Dee, Nick
    Dougherty, Elizabeth L
    Doyle, Wayne I
    Dudoit, Sandrine
    Fang, Rongxin
    Felix, Victor
    Fong, Olivia
    Giglio, Michelle
    Goldy, Jeff
    Hawrylycz, Mike
    Herb, Brian R
    Hertzano, Ronna
    Hou, Xiaomeng
    Hu, Qiwen
    Kancherla, Jayaram
    Kroll, Matthew
    Lathia, Kanan
    Li, Yang Eric
    Lucero, Jacinta D
    Luo, Chongyuan
    Mahurkar, Anup
    McMillen, Delissa
    Nadaf, Naeem M
    Nery, Joseph R
    Nguyen, Thuc Nghi
    Niu, Sheng-Yong
    Ntranos, Vasilis
    Orvis, Joshua
    Osteen, Julia K
    Pham, Thanh
    Pinto-Duarte, Antonio
    Poirion, Olivier
    Preissl, Sebastian
    Purdom, Elizabeth
    Rimorin, Christine
    Risso, Davide
    Rivkin, Angeline C
    Smith, Kimberly
    Street, Kelly
    Sulc, Josef
    Svensson, Valentine
    Tieu, Michael
    Torkelson, Amy
    Tung, Herman
    Vaishnav, Eeshit Dhaval
    Vanderburg, Charles R
    van Velthoven, Cindy
    Wang, Xinxin
    White, Owen R
    Huang, Z Josh
    Kharchenko, Peter V
    Pachter, Lior
    Ngai, John
    Regev, Aviv
    Tasic, Bosiljka
    Welch, Joshua D
    Gillis, Jesse
    Macosko, Evan Z
    Ren, Bing
    Ecker, Joseph R
    Zeng, Hongkui
    Mukamel, Eran A
    Show allShow less

    Date
    2021-10-06
    Journal
    Nature
    Publisher
    Springer Nature
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.1038/s41586-021-03500-8
    Abstract
    Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.
    Rights/Terms
    © 2021. The Author(s).
    Keyword
    Motor Cortex
    Epigenome
    Transcriptome
    Mice
    Atlas
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/16884
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41586-021-03500-8
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