Transcriptional landscape of the prenatal human brain

Jeremy A. Miller, Song-Lin Ding, Susan M. Sunkin, Kimberly A. Smith, Lydia Ng, Aaron Szafer, Amanda Ebbert, Zackery L. Riley, Joshua J. Royall, Kaylynn Aiona, James M. Arnold, Crissa Bennet, Darren Bertagnolli, Krissy Brouner, Stephanie Butler, Shiella Caldejon, Anita Carey, Christine Cuhaciyan, Rachel A. Dalley, Nick Dee, Tim A. Dolbeare, Benjamin A. C. Facer, David Feng, Tim P. Fliss, Garrett Gee, Jeff Goldy, Lindsey Gourley, Benjamin W. Gregor, Guangyu Gu, Robert E. Howard, Jayson M. Jochim, Chihchau L. Kuan, Christopher Lau, Chang-Kyu Lee, Felix Lee, Tracy A. Lemon, Phil Lesnar, Bergen McMurray, Naveed Mastan, Nerick Mosqueda, Theresa Naluai-Cecchini, Nhan-Kiet Ngo, Julie Nyhus, Aaron Oldre, Eric Olson, Jody Parente, Patrick D. Parker, Sheana E. Parry, Allison Stevens, Mihovil Pletikos, Melissa Reding, Kate Roll, David Sandman, Melaine Sarreal, Sheila Shapouri, Nadiya V. Shapovalova, Elaine H. Shen, Nathan Sjoquist, Clifford R. Slaughterbeck, Michael Smith, Andy J. Sodt, Derric Williams, Lilla Zöllei, Bruce Fischl, Mark B. Gerstein, Daniel H. Geschwind, Ian A. Glass, Michael J. Hawrylycz, Robert F. Hevner, Hao Huang, Allan R. Jones, James A. Knowles, Pat Levitt, John W. Phillips, Nenad Šestan, Paul Wohnoutka, Chinh Dang, Amy Bernard, John G. Hohmann and Ed S. Lein ()
Additional contact information
Jeremy A. Miller: Allen Institute for Brain Science
Song-Lin Ding: Allen Institute for Brain Science
Susan M. Sunkin: Allen Institute for Brain Science
Kimberly A. Smith: Allen Institute for Brain Science
Lydia Ng: Allen Institute for Brain Science
Aaron Szafer: Allen Institute for Brain Science
Amanda Ebbert: Allen Institute for Brain Science
Zackery L. Riley: Allen Institute for Brain Science
Joshua J. Royall: Allen Institute for Brain Science
Kaylynn Aiona: Allen Institute for Brain Science
James M. Arnold: Allen Institute for Brain Science
Crissa Bennet: Allen Institute for Brain Science
Darren Bertagnolli: Allen Institute for Brain Science
Krissy Brouner: Allen Institute for Brain Science
Stephanie Butler: Allen Institute for Brain Science
Shiella Caldejon: Allen Institute for Brain Science
Anita Carey: Allen Institute for Brain Science
Christine Cuhaciyan: Allen Institute for Brain Science
Rachel A. Dalley: Allen Institute for Brain Science
Nick Dee: Allen Institute for Brain Science
Tim A. Dolbeare: Allen Institute for Brain Science
Benjamin A. C. Facer: Allen Institute for Brain Science
David Feng: Allen Institute for Brain Science
Tim P. Fliss: Allen Institute for Brain Science
Garrett Gee: Allen Institute for Brain Science
Jeff Goldy: Allen Institute for Brain Science
Lindsey Gourley: Allen Institute for Brain Science
Benjamin W. Gregor: Allen Institute for Brain Science
Guangyu Gu: Allen Institute for Brain Science
Robert E. Howard: Allen Institute for Brain Science
Jayson M. Jochim: Allen Institute for Brain Science
Chihchau L. Kuan: Allen Institute for Brain Science
Christopher Lau: Allen Institute for Brain Science
Chang-Kyu Lee: Allen Institute for Brain Science
Felix Lee: Allen Institute for Brain Science
Tracy A. Lemon: Allen Institute for Brain Science
Phil Lesnar: Allen Institute for Brain Science
Bergen McMurray: Allen Institute for Brain Science
Naveed Mastan: Allen Institute for Brain Science
Nerick Mosqueda: Allen Institute for Brain Science
Theresa Naluai-Cecchini: University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
Nhan-Kiet Ngo: Allen Institute for Brain Science
Julie Nyhus: Allen Institute for Brain Science
Aaron Oldre: Allen Institute for Brain Science
Eric Olson: Allen Institute for Brain Science
Jody Parente: Allen Institute for Brain Science
Patrick D. Parker: Allen Institute for Brain Science
Sheana E. Parry: Allen Institute for Brain Science
Allison Stevens: Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital
Mihovil Pletikos: Yale School of Medicine
Melissa Reding: Allen Institute for Brain Science
Kate Roll: Allen Institute for Brain Science
David Sandman: Allen Institute for Brain Science
Melaine Sarreal: Allen Institute for Brain Science
Sheila Shapouri: Allen Institute for Brain Science
Nadiya V. Shapovalova: Allen Institute for Brain Science
Elaine H. Shen: Allen Institute for Brain Science
Nathan Sjoquist: Allen Institute for Brain Science
Clifford R. Slaughterbeck: Allen Institute for Brain Science
Michael Smith: Allen Institute for Brain Science
Andy J. Sodt: Allen Institute for Brain Science
Derric Williams: Allen Institute for Brain Science
Lilla Zöllei: Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital
Bruce Fischl: Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital
Mark B. Gerstein: Program in Computational Biology and Bioinformatics, Yale University
Daniel H. Geschwind: Program in Neurogenetics, UCLA
Ian A. Glass: University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
Michael J. Hawrylycz: Allen Institute for Brain Science
Robert F. Hevner: Center for Integrative Brain Research, Seattle Children’s Research Institute
Hao Huang: Advanced Imaging Research Center, UT Southwestern Medical Center
Allan R. Jones: Allen Institute for Brain Science
James A. Knowles: Zilkha Neurogenetic Institute, University of Southern California
Pat Levitt: Children’s Hospital
John W. Phillips: Allen Institute for Brain Science
Nenad Šestan: Yale School of Medicine
Paul Wohnoutka: Allen Institute for Brain Science
Chinh Dang: Allen Institute for Brain Science
Amy Bernard: Allen Institute for Brain Science
John G. Hohmann: Allen Institute for Brain Science
Ed S. Lein: Allen Institute for Brain Science

Nature, 2014, vol. 508, issue 7495, 199-206

Abstract: Abstract The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Date: 2014
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DOI: 10.1038/nature13185

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