Rxivist logo

A multimodal cell census and atlas of the mammalian primary motor cortex

By BRAIN Initiative Cell Census Network (BICCN), Ricky S. Adkins, Andrew I. Aldridge, Shona Allen, Seth A. Ament, Xu An, Ethan Armand, Giorgio A Ascoli, Trygve E. Bakken, Anita Bandrowski, Samik Banerjee, Nikolaos Barkas, Anna Bartlett, Helen S. Bateup, M. Margarita Behrens, Philipp Berens, Jim Berg, Matteo Bernabucci, Yves Bernaerts, Darren Bertagnolli, Tommaso Biancalani, Lara Boggeman, A. Sina Booeshaghi, Ian Bowman, Héctor Corrada Bravo, Cathryn René Cadwell, Edward M Callaway, Benjamin Carlin, Carolyn O'Connor, Robert Carter, Tamara Casper, Rosa G. Castanon, Jesus Ramon Castro, Rebecca K Chance, Apaala Chatterjee, Huaming Chen, Jerold Chun, Carlo Colantuoni, Jonathan Crabtree, Heather Creasy, Kirsten Chrichton, Megan Crow, Florence D. D'Orazi, Tanya L Daigle, Rachel Dalley, Nick Dee, Kylee Degatano, Benjamin K. Dichter, Dinh Diep, Liya Ding, Song-Lin Ding, Bertha Dominguez, Hongwei Dong, Weixiu Dong, Elizabeth L. Dougherty, Sandrine Dudoit, Joseph R. Ecker, Stephen W Eichhorn, Rongxin Fang, Victor Felix, Guoping Feng, Zhao Feng, Stephan Fischer, Conor Fitzpatrick, Olivia Fong, Nicholas N. Foster, William Galbavy, James C. Gee, Satrajit S Ghosh, Michelle Giglio, Tom Gillespie, Jesse Gillis, Melissa Goldman, Jeff Goldy, Hui Gong, Lin Gou, Michael Grauer, Yaroslav O Halchenko, Julie A Harris, Leonard Hartmanis, Joshua T. Hatfield, Michael Hawrylycz, Brian Helba, Brian R. Herb, Ronna Hertzano, Houri Hintiryan, Karla E. Hirokawa, Dirk Hockemeyer, Rebecca D. Hodge, Greg Hood, Gregory D Horwitz, Xiaomeng Hou, Lijuan Hu, Qiwen Hu, Z. Josh Huang, Bingxing Huo, Tony Ito-Cole, Matthew Jacobs, Xueyan Jia, Shengdian Jiang, Tao Jiang, Xiaolong Jiang, Xin Jin, Nikolas L. Jorstad, Brian E Kalmbach, Jayaram Kancherla, C. Dirk Keene, Kathleen Kelly, Farzaneh Khajouei, Peter V. Kharchenko, Gukhan Kim, Andrew L. Ko, Dmitry Kobak, Kishori Konwar, Daniel J. Kramer, Fenna M. Krienen, Matthew Kroll, Xiuli Kuang, Hsien-Chi Kuo, Blue B. Lake, Rachael Larsen, Kanan Lathia, Sophie Laturnus, Angus Y Lee, Cheng-Ta Lee, Kuo-Fen Lee, Ed Lein, Phil Lesnar, Anan Li, Xiangning Li, Xu Li, Yang Eric Li, Yaoyao Li, Yuanyuan Li, Byungkook Lim, Sten Linnarsson, Christine S. Liu, Hanqing Liu, Lijuan Liu, Jacinta D. Lucero, Chongyuan Luo, Qingming Luo, Evan Z Macosko, Anup Mahurkar, Maryann E Martone, Katherine S.H. Matho, Steven A McCarroll, Carrie McCracken, Delissa McMillen, Elanine Miranda, Partha Pratim Mitra, Paula Assakura Miyazaki, Judith Mizrachi, Stephanie Mok, Eran A Mukamel, Shalaka Mulherkar, Naeem Nadaf, Maitham Naeemi, Arun Narasimhan, Joseph R. Nery, Lydia Ng, John Ngai, Thuc Nghi Nguyen, Lance Nickel, Philip R Nicovich, Sheng-Yong Niu, Vasilis Ntranos, Michael Nunn, Dustin Olley, Joshua Orvis, Julia K. Osteen, Pavel Osten, Scott F. Owen, Lior Pachter, Ramesh Palaniswamy, Carter R. Palmer, Yan Pang, Hanchuan Peng, Trangthanh Pham, Antonio Pinto-Duarte, Nongluk Plongthongkum, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Lei Qu, Mohammad Rashid, Nora M. Reed, Aviv Regev, Bing Ren, Miao Ren, Christine Rimorin, Davide Risso, Angeline C. Rivkin, Rodrigo Muñoz-Castañeda, William J. Romanow, Alexander J. Ropelewski, Hector Roux de Bézieux, Zongcai Ruan, Rickard Sandberg, Steven Savoia, Federico Scala, Michael Schor, Elise Shen, Kimberly Siletti, Jared B. Smith, Kimberly Smith, Saroja Somasundaram, Yuanyuan Song, Staci Sorensen, David A. Stafford, Kelly N Street, Josef Sulc, Susan Sunkin, Valentine Svensson, Pengcheng Tan, Zheng Huan Tan, Bosiljka Tasic, Carol Thompson, Wei Tian, Timothy L. Tickle, Michael Tieu, Jonathan T Ting, Andreas Tolias, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Koen Van den Berge, Cindy T.J. van Velthoven, Charles R. Vanderburg, Matthew B Veldman, Minh Vu, Wayne Wakeman, Peng Wang, Quanxin Wang, Xinxin Wang, Yimin Wang, Yun Wang, Joshua D Welch, Owen White, Elora W Williams, Fangming Xie, Xie Peng, Feng Xiong, X. William Yang, Anna Marie Yanny, Zizhen Yao, Lulu Yin, Yang Yu, Jing Yuan, Hongkui Zeng, Kun Zhang, Meng Zhang, Zhuzhu Zhang, Sujun Zhao, Xuan Zhao, Jingtian Zhou, Xiaowei Zhuang, Brian Zingg

Posted 21 Oct 2020
bioRxiv DOI: 10.1101/2020.10.19.343129

We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties. ### Competing Interest Statement The competing interests are detailed in the Competing Interests section in the manuscript file.

Download data

  • Downloaded 3,542 times
  • Download rankings, all-time:
    • Site-wide: 3,261
    • In neuroscience: 254
  • Year to date:
    • Site-wide: 1,729
  • Since beginning of last month:
    • Site-wide: 2,677

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News