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1. Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author

Bakken, Trygve E, Jorstad, Nikolas L, Hu, Qiwen, Lake, Blue B, Tian, Wei, Kalmbach, Brian E, Crow, Megan, Hodge, Rebecca D, Krienen, Fenna M, Sorensen, Staci A, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D, Aldridge, Andrew I, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa G, Crichton, Kirsten, Daigle, Tanya L, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T, Herb, Brian R, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine S, Liu, Hanqing, Lucero, Jacinta D, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A, Moussa, Marmar, Nery, Joseph R, Nicovich, Philip R, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K, Owen, Scott, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M, Rimorin, Christine, Rivkin, Angeline, Romanow, William J, Sedeño-Cortés, Adriana E, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A, Behrens, M Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R, Höllt, Thomas, Horwitz, Gregory D, Keene, C Dirk, Kharchenko, Peter V, Ko, Andrew L, Lelieveldt, Boudewijn P, Luo, Chongyuan, Mukamel, Eran A, Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H, Smith, Kimberly, Spain, William J, White, Owen R, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z, McCarroll, Steven A, and Ting, Jonathan T

Subjects
Human Genome, Neurosciences, Genetics, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Atlases as Topic, Callithrix, Epigenesis, Genetic, Epigenomics, Female, GABAergic Neurons, Gene Expression Profiling, Glutamates, Humans, In Situ Hybridization, Fluorescence, Male, Mice, Middle Aged, Motor Cortex, Neurons, Organ Specificity, Phylogeny, Single-Cell Analysis, Species Specificity, Transcriptome, General Science & Technology
Abstract

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

Published
2021

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

Author

Callaway, Edward M, Dong, Hong-Wei, Ecker, Joseph R, Hawrylycz, Michael J, Huang, Z Josh, Lein, Ed S, Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A, Behrens, M Margarita, Chun, Jerold, Feng, Guoping, Gee, James C, Ghosh, Satrajit S, Halchenko, Yaroslav O, Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E, Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J, Tickle, Timothy L, Yang, X William, Zhang, Kun, Bakken, Trygve E, Berens, Philipp, Daigle, Tanya L, Harris, Julie A, Jorstad, Nikolas L, Kalmbach, Brian E, Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S, Mukamel, Eran A, Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T, Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L, Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D, Hu, Lijuan, Keene, C Dirk, Krienen, Fenna M, Kroll, Matthew, Lake, Blue B, Lathia, Kanan, Linnarsson, Sten, Liu, Christine S, Macosko, Evan Z, McCarroll, Steven A, McMillen, Delissa, Nadaf, Naeem M, Nguyen, Thuc Nghi, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M, Regev, Aviv, Rimorin, Christine, Romanow, William J, Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy TJ, Vanderburg, Charles R, Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D, Osteen, Julia K, Pinto-Duarte, Antonio, and Poirion, Olivier

Subjects
Genetics, Neurosciences, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Atlases as Topic, Callithrix, Epigenomics, Female, Gene Expression Profiling, Glutamates, Humans, In Situ Hybridization, Fluorescence, Male, Mice, Motor Cortex, Neurons, Organ Specificity, Phylogeny, Single-Cell Analysis, Species Specificity, Transcriptome, BRAIN Initiative Cell Census Network, General Science & Technology
Abstract

Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex 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. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

Published
2021

3. Conserved cell types with divergent features in human versus mouse cortex.

Author

Hodge, Rebecca D, Bakken, Trygve E, Miller, Jeremy A, Smith, Kimberly A, Barkan, Eliza R, Graybuck, Lucas T, Close, Jennie L, Long, Brian, Johansen, Nelson, Penn, Osnat, Yao, Zizhen, Eggermont, Jeroen, Höllt, Thomas, Levi, Boaz P, Shehata, Soraya I, Aevermann, Brian, Beller, Allison, Bertagnolli, Darren, Brouner, Krissy, Casper, Tamara, Cobbs, Charles, Dalley, Rachel, Dee, Nick, Ding, Song-Lin, Ellenbogen, Richard G, Fong, Olivia, Garren, Emma, Goldy, Jeff, Gwinn, Ryder P, Hirschstein, Daniel, Keene, C Dirk, Keshk, Mohamed, Ko, Andrew L, Lathia, Kanan, Mahfouz, Ahmed, Maltzer, Zoe, McGraw, Medea, Nguyen, Thuc Nghi, Nyhus, Julie, Ojemann, Jeffrey G, Oldre, Aaron, Parry, Sheana, Reynolds, Shannon, Rimorin, Christine, Shapovalova, Nadiya V, Somasundaram, Saroja, Szafer, Aaron, Thomsen, Elliot R, Tieu, Michael, Quon, Gerald, Scheuermann, Richard H, Yuste, Rafael, Sunkin, Susan M, Lelieveldt, Boudewijn, Feng, David, Ng, Lydia, Bernard, Amy, Hawrylycz, Michael, Phillips, John W, Tasic, Bosiljka, Zeng, Hongkui, Jones, Allan R, Koch, Christof, and Lein, Ed S

Subjects
Cerebral Cortex, Astrocytes, Neurons, Animals, Humans, Mice, Species Specificity, Neural Inhibition, Principal Component Analysis, Adolescent, Adult, Aged, Middle Aged, Female, Male, Young Adult, Biological Evolution, Single-Cell Analysis, Transcriptome, RNA-Seq, Genetics, Neurosciences, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Neurological, General Science & Technology
Abstract

Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain.

Published
2019

4. A comprehensive transcriptional map of primate brain development.

Author

Bakken, Trygve E, Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Dalley, Rachel A, Royall, Joshua J, Lemon, Tracy, Shapouri, Sheila, Aiona, Kaylynn, Arnold, James, Bennett, Jeffrey L, Bertagnolli, Darren, Bickley, Kristopher, Boe, Andrew, Brouner, Krissy, Butler, Stephanie, Byrnes, Emi, Caldejon, Shiella, Carey, Anita, Cate, Shelby, Chapin, Mike, Chen, Jefferey, Dee, Nick, Desta, Tsega, Dolbeare, Tim A, Dotson, Nadia, Ebbert, Amanda, Fulfs, Erich, Gee, Garrett, Gilbert, Terri L, Goldy, Jeff, Gourley, Lindsey, Gregor, Ben, Gu, Guangyu, Hall, Jon, Haradon, Zeb, Haynor, David R, Hejazinia, Nika, Hoerder-Suabedissen, Anna, Howard, Robert, Jochim, Jay, Kinnunen, Marty, Kriedberg, Ali, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Luong, Lon, Mastan, Naveed, May, Ryan, Melchor, Jose, Mosqueda, Nerick, Mott, Erika, Ngo, Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana, Pendergraft, Julie, Potekhina, Lydia, Reding, Melissa, Riley, Zackery L, Roberts, Tyson, Rogers, Brandon, Roll, Kate, Rosen, David, Sandman, David, Sarreal, Melaine, Shapovalova, Nadiya, Shi, Shu, Sjoquist, Nathan, Sodt, Andy J, Townsend, Robbie, Velasquez, Lissette, Wagley, Udi, Wakeman, Wayne B, White, Cassandra, Bennett, Crissa, Wu, Jennifer, Young, Rob, Youngstrom, Brian L, Wohnoutka, Paul, Gibbs, Richard A, Rogers, Jeffrey, Hohmann, John G, Hawrylycz, Michael J, Hevner, Robert F, Molnár, Zoltán, Phillips, John W, Dang, Chinh, Jones, Allan R, Amaral, David G, Bernard, Amy, and Lein, Ed S

Subjects
Brain, Neocortex, Animals, Macaca mulatta, Humans, Microcephaly, Risk Factors, Schizophrenia, Cell Adhesion, Species Specificity, Transcription, Genetic, Conserved Sequence, Aging, Female, Male, Neurogenesis, Intellectual Disability, Transcriptome, Spatio-Temporal Analysis, Autism Spectrum Disorder, Neurodevelopmental Disorders, Transcription, Genetic, General Science & Technology
Abstract

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Published
2016

5. Transcriptional landscape of the prenatal human brain.

Author

Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Ebbert, Amanda, Riley, Zackery L, Royall, Joshua J, Aiona, Kaylynn, Arnold, James M, Bennet, Crissa, Bertagnolli, Darren, Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Carey, Anita, Cuhaciyan, Christine, Dalley, Rachel A, Dee, Nick, Dolbeare, Tim A, Facer, Benjamin AC, Feng, David, Fliss, Tim P, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W, Gu, Guangyu, Howard, Robert E, Jochim, Jayson M, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Lemon, Tracy A, Lesnar, Phil, McMurray, Bergen, Mastan, Naveed, Mosqueda, Nerick, Naluai-Cecchini, Theresa, Ngo, Nhan-Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana E, Stevens, Allison, Pletikos, Mihovil, Reding, Melissa, Roll, Kate, Sandman, David, Sarreal, Melaine, Shapouri, Sheila, Shapovalova, Nadiya V, Shen, Elaine H, Sjoquist, Nathan, Slaughterbeck, Clifford R, Smith, Michael, Sodt, Andy J, Williams, Derric, Zöllei, Lilla, Fischl, Bruce, Gerstein, Mark B, Geschwind, Daniel H, Glass, Ian A, Hawrylycz, Michael J, Hevner, Robert F, Huang, Hao, Jones, Allan R, Knowles, James A, Levitt, Pat, Phillips, John W, Sestan, Nenad, Wohnoutka, Paul, Dang, Chinh, Bernard, Amy, Hohmann, John G, and Lein, Ed S

Subjects
Brain, Neocortex, Fetus, Animals, Humans, Mice, Anatomy, Artistic, Species Specificity, Gene Expression Regulation, Developmental, Conserved Sequence, Gene Regulatory Networks, Atlases as Topic, Transcriptome, Anatomy, Artistic, Gene Expression Regulation, Developmental, General Science & Technology
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.

Published
2014

6. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Author

Yao, Zizhen, primary, van Velthoven, Cindy T. J., additional, Kunst, Michael, additional, Zhang, Meng, additional, McMillen, Delissa, additional, Lee, Changkyu, additional, Jung, Won, additional, Goldy, Jeff, additional, Abdelhak, Aliya, additional, Aitken, Matthew, additional, Baker, Katherine, additional, Baker, Pamela, additional, Barkan, Eliza, additional, Bertagnolli, Darren, additional, Bhandiwad, Ashwin, additional, Bielstein, Cameron, additional, Bishwakarma, Prajal, additional, Campos, Jazmin, additional, Carey, Daniel, additional, Casper, Tamara, additional, Chakka, Anish Bhaswanth, additional, Chakrabarty, Rushil, additional, Chavan, Sakshi, additional, Chen, Min, additional, Clark, Michael, additional, Close, Jennie, additional, Crichton, Kirsten, additional, Daniel, Scott, additional, DiValentin, Peter, additional, Dolbeare, Tim, additional, Ellingwood, Lauren, additional, Fiabane, Elysha, additional, Fliss, Timothy, additional, Gee, James, additional, Gerstenberger, James, additional, Glandon, Alexandra, additional, Gloe, Jessica, additional, Gould, Joshua, additional, Gray, James, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hirschstein, Daniel, additional, Ho, Windy, additional, Hooper, Marcus, additional, Huang, Mike, additional, Hupp, Madie, additional, Jin, Kelly, additional, Kroll, Matthew, additional, Lathia, Kanan, additional, Leon, Arielle, additional, Li, Su, additional, Long, Brian, additional, Madigan, Zach, additional, Malloy, Jessica, additional, Malone, Jocelin, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, McGinty, Ryan, additional, Mei, Nicholas, additional, Melchor, Jose, additional, Meyerdierks, Emma, additional, Mollenkopf, Tyler, additional, Moonsman, Skyler, additional, Nguyen, Thuc Nghi, additional, Otto, Sven, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Sanchez, Raymond, additional, Sawyer, Lane, additional, Shapovalova, Nadiya, additional, Shepard, Noah, additional, Slaughterbeck, Cliff, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Valera Cuevas, Nasmil, additional, Vance, Shane, additional, Wadhwani, Katherine, additional, Ward, Katelyn, additional, Levi, Boaz, additional, Farrell, Colin, additional, Young, Rob, additional, Staats, Brian, additional, Wang, Ming-Qiang Michael, additional, Thompson, Carol L., additional, Mufti, Shoaib, additional, Pagan, Chelsea M., additional, Kruse, Lauren, additional, Dee, Nick, additional, Sunkin, Susan M., additional, Esposito, Luke, additional, Hawrylycz, Michael J., additional, Waters, Jack, additional, Ng, Lydia, additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Zhuang, Xiaowei, additional, and Zeng, Hongkui, additional

Published
2023
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7. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author

Bakken, Trygve E., primary, Jorstad, Nikolas L., additional, Hu, Qiwen, additional, Lake, Blue B., additional, Tian, Wei, additional, Kalmbach, Brian E., additional, Crow, Megan, additional, Hodge, Rebecca D., additional, Krienen, Fenna M., additional, Sorensen, Staci A., additional, Eggermont, Jeroen, additional, Yao, Zizhen, additional, Aevermann, Brian D., additional, Aldridge, Andrew I., additional, Bartlett, Anna, additional, Bertagnolli, Darren, additional, Casper, Tamara, additional, Castanon, Rosa G., additional, Crichton, Kirsten, additional, Daigle, Tanya L., additional, Dalley, Rachel, additional, Dee, Nick, additional, Dembrow, Nikolai, additional, Diep, Dinh, additional, Ding, Song-Lin, additional, Dong, Weixiu, additional, Fang, Rongxin, additional, Fischer, Stephan, additional, Goldman, Melissa, additional, Goldy, Jeff, additional, Graybuck, Lucas T., additional, Herb, Brian R., additional, Hou, Xiaomeng, additional, Kancherla, Jayaram, additional, Kroll, Matthew, additional, Lathia, Kanan, additional, van Lew, Baldur, additional, Li, Yang Eric, additional, Liu, Christine S., additional, Liu, Hanqing, additional, Lucero, Jacinta D., additional, Mahurkar, Anup, additional, McMillen, Delissa, additional, Miller, Jeremy A., additional, Moussa, Marmar, additional, Nery, Joseph R., additional, Nicovich, Philip R., additional, Niu, Sheng-Yong, additional, Orvis, Joshua, additional, Osteen, Julia K., additional, Owen, Scott, additional, Palmer, Carter R., additional, Pham, Thanh, additional, Plongthongkum, Nongluk, additional, Poirion, Olivier, additional, Reed, Nora M., additional, Rimorin, Christine, additional, Rivkin, Angeline, additional, Romanow, William J., additional, Sedeño-Cortés, Adriana E., additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Wang, Xinxin, additional, Xie, Fangming, additional, Yanny, Anna Marie, additional, Zhang, Renee, additional, Ament, Seth A., additional, Behrens, M. Margarita, additional, Bravo, Hector Corrada, additional, Chun, Jerold, additional, Dobin, Alexander, additional, Gillis, Jesse, additional, Hertzano, Ronna, additional, Hof, Patrick R., additional, Höllt, Thomas, additional, Horwitz, Gregory D., additional, Keene, C. Dirk, additional, Kharchenko, Peter V., additional, Ko, Andrew L., additional, Lelieveldt, Boudewijn P., additional, Luo, Chongyuan, additional, Mukamel, Eran A., additional, Pinto-Duarte, António, additional, Preiss, Sebastian, additional, Regev, Aviv, additional, Ren, Bing, additional, Scheuermann, Richard H., additional, Smith, Kimberly, additional, Spain, William J., additional, White, Owen R., additional, Koch, Christof, additional, Hawrylycz, Michael, additional, Tasic, Bosiljka, additional, Macosko, Evan Z., additional, McCarroll, Steven A., additional, Ting, Jonathan T., additional, Zeng, Hongkui, additional, Zhang, Kun, additional, Feng, Guoping, additional, Ecker, Joseph R., additional, Linnarsson, Sten, additional, and Lein, Ed S., additional

Published
2022
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8. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Author

Berg, Jim, primary, Sorensen, Staci A., additional, Ting, Jonathan T., additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Buchin, Anatoly, additional, Bakken, Trygve E., additional, Budzillo, Agata, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gouwens, Nathan W., additional, Hodge, Rebecca D., additional, Kalmbach, Brian, additional, Lee, Changkyu, additional, Lee, Brian R., additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Barkan, Eliza, additional, Beller, Allison, additional, Berry, Kyla, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bomben, Jasmine, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Chong, Peter, additional, Crichton, Kirsten, additional, Dalley, Rachel, additional, de Frates, Rebecca, additional, Desta, Tsega, additional, Lee, Samuel Dingman, additional, D’Orazi, Florence, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Farrell, Colin, additional, Feng, David, additional, Fong, Olivia, additional, Furdan, Szabina, additional, Galakhova, Anna A., additional, Gamlin, Clare, additional, Gary, Amanda, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Gorham, Melissa, additional, Goriounova, Natalia A., additional, Gratiy, Sergey, additional, Graybuck, Lucas, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hansen, Nathan, additional, Heistek, Tim S., additional, Henry, Alex M., additional, Heyer, Djai B., additional, Hill, DiJon, additional, Hill, Chris, additional, Hupp, Madie, additional, Jarsky, Tim, additional, Kebede, Sara, additional, Keene, Lisa, additional, Kim, Lisa, additional, Kim, Mean-Hwan, additional, Kroll, Matthew, additional, Latimer, Caitlin, additional, Levi, Boaz P., additional, Link, Katherine E., additional, Mallory, Matthew, additional, Mann, Rusty, additional, Marshall, Desiree, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica, additional, Mertens, Eline J., additional, Mezei, Leona, additional, Mihut, Norbert, additional, Mok, Stephanie, additional, Molnar, Gabor, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Nyhus, Julie, additional, Olah, Gaspar, additional, Oldre, Aaron, additional, Omstead, Victoria, additional, Ozsvar, Attila, additional, Park, Daniel, additional, Peng, Hanchuan, additional, Pham, Trangthanh, additional, Pom, Christina A., additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Ransford, Shea, additional, Reid, David, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Sandman, David, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Szafer, Aaron, additional, Szemenyei, Viktor, additional, Thomsen, Elliot R., additional, Tieu, Michael, additional, Torkelson, Amy, additional, Trinh, Jessica, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Waleboer, Femke, additional, Ward, Katelyn, additional, Wilbers, René, additional, Williams, Grace, additional, Yao, Zizhen, additional, Yoon, Jae-Geun, additional, Anastassiou, Costas, additional, Arkhipov, Anton, additional, Barzo, Pal, additional, Bernard, Amy, additional, Cobbs, Charles, additional, de Witt Hamer, Philip C., additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gwinn, Ryder P., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Idema, Sander, additional, Jones, Allan R., additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Murphy, Gabe J., additional, Ng, Lydia, additional, Ojemann, Jeffrey G., additional, Patel, Anoop P., additional, Phillips, John W., additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Yuste, Rafael, additional, Segev, Idan, additional, de Kock, Christiaan P. J., additional, Mansvelder, Huibert D., additional, Tamas, Gabor, additional, Zeng, Hongkui, additional, Koch, Christof, additional, and Lein, Ed S., additional

Published
2022
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9. A mesoscale connectome of the mouse brain

Author

Oh, Seung Wook, Harris, Julie A., Ng, Lydia, Winslow, Brent, Cain, Nicholas, Mihalas, Stefan, Wang, Quanxin, Lau, Chris, Kuan, Leonard, Henry, Alex M., Mortrud, Marty T., Ouellette, Benjamin, Nguyen, Thuc Nghi, Sorensen, Staci A., Slaughterbeck, Clifford R., Wakeman, Wayne, Li, Yang, Feng, David, Ho, Anh, Nicholas, Eric, Hirokawa, Karla E., Bohn, Phillip, Joines, Kevin M., Peng, Hanchuan, Hawrylycz, Michael J., Phillips, John W., Hohmann, John G., Wohnoutka, Paul, Gerfen, Charles R., Koch, Christof, Bernard, Amy, Dang, Chinh, Jones, Allan R., and Zeng, Hongkui

Subjects
Brain -- Research -- Physiological aspects, Neural circuitry -- Research -- Physiological aspects, Enhanced green fluorescent protein -- Research -- Physiological aspects, Computer simulation -- Usage, Computer-generated environments -- Usage, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease., A central principle of neuroscience is that the nervous system is a network of diverse types of neurons and supporting cells communicating with each other mainly through synaptic connections. This [...]

Published
2014
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10. Morphological diversity of single neurons in molecularly defined cell types

Author

Peng, Hanchuan, primary, Xie, Peng, additional, Liu, Lijuan, additional, Kuang, Xiuli, additional, Wang, Yimin, additional, Qu, Lei, additional, Gong, Hui, additional, Jiang, Shengdian, additional, Li, Anan, additional, Ruan, Zongcai, additional, Ding, Liya, additional, Yao, Zizhen, additional, Chen, Chao, additional, Chen, Mengya, additional, Daigle, Tanya L., additional, Dalley, Rachel, additional, Ding, Zhangcan, additional, Duan, Yanjun, additional, Feiner, Aaron, additional, He, Ping, additional, Hill, Chris, additional, Hirokawa, Karla E., additional, Hong, Guodong, additional, Huang, Lei, additional, Kebede, Sara, additional, Kuo, Hsien-Chi, additional, Larsen, Rachael, additional, Lesnar, Phil, additional, Li, Longfei, additional, Li, Qi, additional, Li, Xiangning, additional, Li, Yaoyao, additional, Li, Yuanyuan, additional, Liu, An, additional, Lu, Donghuan, additional, Mok, Stephanie, additional, Ng, Lydia, additional, Nguyen, Thuc Nghi, additional, Ouyang, Qiang, additional, Pan, Jintao, additional, Shen, Elise, additional, Song, Yuanyuan, additional, Sunkin, Susan M., additional, Tasic, Bosiljka, additional, Veldman, Matthew B., additional, Wakeman, Wayne, additional, Wan, Wan, additional, Wang, Peng, additional, Wang, Quanxin, additional, Wang, Tao, additional, Wang, Yaping, additional, Xiong, Feng, additional, Xiong, Wei, additional, Xu, Wenjie, additional, Ye, Min, additional, Yin, Lulu, additional, Yu, Yang, additional, Yuan, Jia, additional, Yuan, Jing, additional, Yun, Zhixi, additional, Zeng, Shaoqun, additional, Zhang, Shichen, additional, Zhao, Sujun, additional, Zhao, Zijun, additional, Zhou, Zhi, additional, Huang, Z. Josh, additional, Esposito, Luke, additional, Hawrylycz, Michael J., additional, Sorensen, Staci A., additional, Yang, X. William, additional, Zheng, Yefeng, additional, Gu, Zhongze, additional, Xie, Wei, additional, Koch, Christof, additional, Luo, Qingming, additional, Harris, Julie A., additional, Wang, Yun, additional, and Zeng, Hongkui, additional

Published
2021
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11. Human neocortical expansion involves glutamatergic neuron diversification

Author

Berg, Jim, primary, Sorensen, Staci A., additional, Ting, Jonathan T., additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Buchin, Anatoly, additional, Bakken, Trygve E., additional, Budzillo, Agata, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gouwens, Nathan W., additional, Hodge, Rebecca D., additional, Kalmbach, Brian, additional, Lee, Changkyu, additional, Lee, Brian R., additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Barkan, Eliza, additional, Beller, Allison, additional, Berry, Kyla, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bomben, Jasmine, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Chong, Peter, additional, Crichton, Kirsten, additional, Dalley, Rachel, additional, de Frates, Rebecca, additional, Desta, Tsega, additional, Lee, Samuel Dingman, additional, D’Orazi, Florence, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Farrell, Colin, additional, Feng, David, additional, Fong, Olivia, additional, Furdan, Szabina, additional, Galakhova, Anna A., additional, Gamlin, Clare, additional, Gary, Amanda, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Gorham, Melissa, additional, Goriounova, Natalia A., additional, Gratiy, Sergey, additional, Graybuck, Lucas, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hansen, Nathan, additional, Heistek, Tim S., additional, Henry, Alex M., additional, Heyer, Djai B., additional, Hill, DiJon, additional, Hill, Chris, additional, Hupp, Madie, additional, Jarsky, Tim, additional, Kebede, Sara, additional, Keene, Lisa, additional, Kim, Lisa, additional, Kim, Mean-Hwan, additional, Kroll, Matthew, additional, Latimer, Caitlin, additional, Levi, Boaz P., additional, Link, Katherine E., additional, Mallory, Matthew, additional, Mann, Rusty, additional, Marshall, Desiree, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica, additional, Mertens, Eline J., additional, Mezei, Leona, additional, Mihut, Norbert, additional, Mok, Stephanie, additional, Molnar, Gabor, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Nyhus, Julie, additional, Olah, Gaspar, additional, Oldre, Aaron, additional, Omstead, Victoria, additional, Ozsvar, Attila, additional, Park, Daniel, additional, Peng, Hanchuan, additional, Pham, Trangthanh, additional, Pom, Christina A., additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Ransford, Shea, additional, Reid, David, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Sandman, David, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Szafer, Aaron, additional, Szemenyei, Viktor, additional, Thomsen, Elliot R., additional, Tieu, Michael, additional, Torkelson, Amy, additional, Trinh, Jessica, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Waleboer, Femke, additional, Ward, Katelyn, additional, Wilbers, René, additional, Williams, Grace, additional, Yao, Zizhen, additional, Yoon, Jae-Geun, additional, Anastassiou, Costas, additional, Arkhipov, Anton, additional, Barzo, Pal, additional, Bernard, Amy, additional, Cobbs, Charles, additional, de Witt Hamer, Philip C., additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gwinn, Ryder P., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Idema, Sander, additional, Jones, Allan R., additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Murphy, Gabe J., additional, Ng, Lydia, additional, Ojemann, Jeffrey G., additional, Patel, Anoop P., additional, Phillips, John W., additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Yuste, Rafael, additional, Segev, Idan, additional, de Kock, Christiaan P. J., additional, Mansvelder, Huibert D., additional, Tamas, Gabor, additional, Zeng, Hongkui, additional, Koch, Christof, additional, and Lein, Ed S., additional

Published
2021
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12. Cellular anatomy of the mouse primary motor cortex

Author

Muñoz-Castañeda, Rodrigo, primary, Zingg, Brian, additional, Matho, Katherine S., additional, Chen, Xiaoyin, additional, Wang, Quanxin, additional, Foster, Nicholas N., additional, Li, Anan, additional, Narasimhan, Arun, additional, Hirokawa, Karla E., additional, Huo, Bingxing, additional, Bannerjee, Samik, additional, Korobkova, Laura, additional, Park, Chris Sin, additional, Park, Young-Gyun, additional, Bienkowski, Michael S., additional, Chon, Uree, additional, Wheeler, Diek W., additional, Li, Xiangning, additional, Wang, Yun, additional, Naeemi, Maitham, additional, Xie, Peng, additional, Liu, Lijuan, additional, Kelly, Kathleen, additional, An, Xu, additional, Attili, Sarojini M., additional, Bowman, Ian, additional, Bludova, Anastasiia, additional, Cetin, Ali, additional, Ding, Liya, additional, Drewes, Rhonda, additional, D’Orazi, Florence, additional, Elowsky, Corey, additional, Fischer, Stephan, additional, Galbavy, William, additional, Gao, Lei, additional, Gillis, Jesse, additional, Groblewski, Peter A., additional, Gou, Lin, additional, Hahn, Joel D., additional, Hatfield, Joshua T., additional, Hintiryan, Houri, additional, Huang, Junxiang Jason, additional, Kondo, Hideki, additional, Kuang, Xiuli, additional, Lesnar, Philip, additional, Li, Xu, additional, Li, Yaoyao, additional, Lin, Mengkuan, additional, Lo, Darrick, additional, Mizrachi, Judith, additional, Mok, Stephanie, additional, Nicovich, Philip R., additional, Palaniswamy, Ramesh, additional, Palmer, Jason, additional, Qi, Xiaoli, additional, Shen, Elise, additional, Sun, Yu-Chi, additional, Tao, Huizhong W., additional, Wakemen, Wayne, additional, Wang, Yimin, additional, Yao, Shenqin, additional, Yuan, Jing, additional, Zhan, Huiqing, additional, Zhu, Muye, additional, Ng, Lydia, additional, Zhang, Li I., additional, Lim, Byung Kook, additional, Hawrylycz, Michael, additional, Gong, Hui, additional, Gee, James C., additional, Kim, Yongsoo, additional, Chung, Kwanghun, additional, Yang, X. William, additional, Peng, Hanchuan, additional, Luo, Qingming, additional, Mitra, Partha P., additional, Zador, Anthony M., additional, Zeng, Hongkui, additional, Ascoli, Giorgio A., additional, Josh Huang, Z., additional, Osten, Pavel, additional, Harris, Julie A., additional, and Dong, Hong-Wei, additional

Published
2021
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13. A mesoscale connectome of the mouse brain

Author

Wook Oh, Seung, Harris, Julie A., Ng, Lydia, Winslow, Brent, Cain, Nicholas, Mihalas, Stefan, Wang, Quanxin, Lau, Chris, Kuan, Leonard, Henry, Alex M., Mortrud, Marty T., Ouellette, Benjamin, Nghi Nguyen, Thuc, Sorensen, Staci A., Slaughterbeck, Clifford R., Wakeman, Wayne, Li, Yang, Feng, David, Ho, Anh, Nicholas, Eric, Hirokawa, Karla E., Bohn, Phillip, Joines, Kevin M., Peng, Hanchuan, Hawrylycz, Michael J., Phillips, John W., Hohmann, John G., Wohnoutka, Paul, Gerfen, Charles R., Koch, Christof, Bernard, Amy, Dang, Chinh, Jones, Allan R., and Zeng, Hongkui

Published
2014
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14. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigo, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C. J., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu1, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermuller, Jorg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K.G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaoz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A., Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W.H., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Hoon Kim, Tae, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N. S., Yu, Yong, Birney*, Ewan, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I. W., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrimsdottir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, Goncalo R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V.B., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Baylor College of Medicine, Human Genome Sequencing Center, Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The ENCODE Project Consortium; Analysis Coordination; Ewan Birney (corresponding author) [1]; John A. Stamatoyannopoulos (corresponding author) [2]; Anindya Dutta (corresponding author) [3]; Roderic Guigó (corresponding author) [4, 5]; Thomas [...]

Published
2007
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15. An anatomically comprehensive atlas of the adult human brain transcriptome

Author

Hawrylycz, Michael J., Lein, Ed S., Guillozet-Bongaarts, Angela L., Shen, Elaine H., Ng, Lydia, Miller, Jeremy A., van de Lagemaat, Louie N., Smith, Kimberly A., Ebbert, Amanda, Riley, Zackery L., Abajian, Chris, Beckmann, Christian F., Bernard, Amy, Bertagnolli, Darren, Boe, Andrew F., Cartagena, Preston M., Chakravarty, Mallar M., Chapin, Mike, Chong, Jimmy, Dalley, Rachel A., Daly, Barry David, Dang, Chinh, Datta, Suvro, Dee, Nick, Dolbeare, Tim A., Faber, Vance, Feng, David, Fowler, David R., Goldy, Jeff, Gregor, Benjamin W., Haradon, Zeb, Haynor, David R., Hohmann, John G., Horvath, Steve, Howard, Robert E., Jeromin, Andreas, Jochim, Jayson M., Kinnunen, Marty, Lau, Christopher, Lazarz, Evan T., Lee, Changkyu, Lemon, Tracy A., Li, Ling, Li, Yang, Morris, John A., Overly, Caroline C., Parker, Patrick D., Parry, Sheana E., Reding, Melissa, Royall, Joshua J., Schulkin, Jay, Sequeira, Pedro Adolfo, Slaughterbeck, Clifford R., Smith, Simon C., Sodt, Andy J., Sunkin, Susan M., Swanson, Beryl E., Vawter, Marquis P., Williams, Derric, Wohnoutka, Paul, Zielke, Ronald H., Geschwind, Daniel H., Hof, Patrick R., Smith, Stephen M., Koch, Christof, Grant, Seth G. N., and Jones, Allan R.

Published
2012
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16. Genome-wide atlas of gene expression in the adult mouse brain

Author

Lein, Ed S., Hawrylycz, Michael J., Ao, Nancy, Ayres, Mikael, Bensinger, Amy, Bernard, Amy, Boe, Andrew F., Boguski, Mark S., Brockway, Kevin S., Byrnes, Emi J., Chen, Lin, Chen, Li, Chen, Tsuey-Ming, Chin, Mei Chi, Chong, Jimmy, Crook, Brian E., Czaplinska, Aneta, Dang, Chinh N., Datta, Suvro, Dee, Nick R., Desaki, Aimee L., Desta, Tsega, Diep, Ellen, Dolbeare, Tim A., Donelan, Matthew J., Dong, Hong-Wei, Dougherty, Jennifer G., Duncan, Ben J., Ebbert, Amanda J., Eichele, Gregor, Estin, Lili K., Faber, Casey, Facer, Benjamin A., Fields, Rick, Fischer, Shanna R., Fliss, Tim P., Frensley, Cliff, Gates, Sabrina N., Glattfelder, Katie J., Halverson, Kevin R., Hart, Matthew R., Hohmann, John G., Howell, Maureen P., Jeung, Darren P., Johnson, Rebecca A., Karr, Patrick T., Kawal, Reena, Kidney, Jolene M., Knapik, Rachel H., Kuan, Chihchau L., Lake, James H., Laramee, Annabel R., Larsen, Kirk D., Lau, Christopher, Lemon, Tracy A., Liang, Agnes J., Liu, Ying, Luong, Lon T., Michaels, Jesse, Morgan, Judith J., Morgan, Rebecca J., Mortrud, Marty T., Mosqueda, Nerick F., Ng, Lydia L., Ng, Randy, Orta, Geralyn J., Overly, Caroline C., Pak, Tu H., Parry, Sheana E., Pathak, Sayan D., Pearson, Owen C., Puchalski, Ralph B., Riley, Zackery L., Rockett, Hannah R., Rowland, Stephen A., Royall, Joshua J., Ruiz, Marcos J., Sarno, Nadia R., Schaffnit, Katherine, Shapovalova, Nadiya V., Sivisay, Taz, Slaughterbeck, Clifford R., Smith, Simon C., Smith, Kimberly A., Smith, Bryan I., Sodt, Andy J., Stewart, Nick N., Stumpf, Kenda-Ruth, Sunkin, Susan M., Sutram, Madhavi, Tam, Angelene, Teemer, Carey D., Thaller, Christina, Thompson, Carol L., Varnam, Lee R., Visel, Axel, Whitlock, Ray M., Wohnoutka, Paul E., Wolkey, Crissa K., Wong, Victoria Y., Wood, Matthew, Yaylaoglu, Murat B., Young, Rob C., Youngstrom, Brian L., Yuan, Xu Feng, Zhang, Bin, Zwingman, Theresa A., and Jones, Allan R.

Published
2007

17. Shared and distinct transcriptomic cell types across neocortical areas

Author

Tasic, Bosiljka, primary, Yao, Zizhen, additional, Graybuck, Lucas T., additional, Smith, Kimberly A., additional, Nguyen, Thuc Nghi, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Garren, Emma, additional, Economo, Michael N., additional, Viswanathan, Sarada, additional, Penn, Osnat, additional, Bakken, Trygve, additional, Menon, Vilas, additional, Miller, Jeremy, additional, Fong, Olivia, additional, Hirokawa, Karla E., additional, Lathia, Kanan, additional, Rimorin, Christine, additional, Tieu, Michael, additional, Larsen, Rachael, additional, Casper, Tamara, additional, Barkan, Eliza, additional, Kroll, Matthew, additional, Parry, Sheana, additional, Shapovalova, Nadiya V., additional, Hirschstein, Daniel, additional, Pendergraft, Julie, additional, Sullivan, Heather A., additional, Kim, Tae Kyung, additional, Szafer, Aaron, additional, Dee, Nick, additional, Groblewski, Peter, additional, Wickersham, Ian, additional, Cetin, Ali, additional, Harris, Julie A., additional, Levi, Boaz P., additional, Sunkin, Susan M., additional, Madisen, Linda, additional, Daigle, Tanya L., additional, Looger, Loren, additional, Bernard, Amy, additional, Phillips, John, additional, Lein, Ed, additional, Hawrylycz, Michael, additional, Svoboda, Karel, additional, Jones, Allan R., additional, Koch, Christof, additional, and Zeng, Hongkui, additional

Published
2018
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18. Genome-wide atlas of gene expression in the adult mouse brain

Author

Lein, Ed S., primary, Hawrylycz, Michael J., additional, Ao, Nancy, additional, Ayres, Mikael, additional, Bensinger, Amy, additional, Bernard, Amy, additional, Boe, Andrew F., additional, Boguski, Mark S., additional, Brockway, Kevin S., additional, Byrnes, Emi J., additional, Chen, Lin, additional, Chen, Li, additional, Chen, Tsuey-Ming, additional, Chi Chin, Mei, additional, Chong, Jimmy, additional, Crook, Brian E., additional, Czaplinska, Aneta, additional, Dang, Chinh N., additional, Datta, Suvro, additional, Dee, Nick R., additional, Desaki, Aimee L., additional, Desta, Tsega, additional, Diep, Ellen, additional, Dolbeare, Tim A., additional, Donelan, Matthew J., additional, Dong, Hong-Wei, additional, Dougherty, Jennifer G., additional, Duncan, Ben J., additional, Ebbert, Amanda J., additional, Eichele, Gregor, additional, Estin, Lili K., additional, Faber, Casey, additional, Facer, Benjamin A., additional, Fields, Rick, additional, Fischer, Shanna R., additional, Fliss, Tim P., additional, Frensley, Cliff, additional, Gates, Sabrina N., additional, Glattfelder, Katie J., additional, Halverson, Kevin R., additional, Hart, Matthew R., additional, Hohmann, John G., additional, Howell, Maureen P., additional, Jeung, Darren P., additional, Johnson, Rebecca A., additional, Karr, Patrick T., additional, Kawal, Reena, additional, Kidney, Jolene M., additional, Knapik, Rachel H., additional, Kuan, Chihchau L., additional, Lake, James H., additional, Laramee, Annabel R., additional, Larsen, Kirk D., additional, Lau, Christopher, additional, Lemon, Tracy A., additional, Liang, Agnes J., additional, Liu, Ying, additional, Luong, Lon T., additional, Michaels, Jesse, additional, Morgan, Judith J., additional, Morgan, Rebecca J., additional, Mortrud, Marty T., additional, Mosqueda, Nerick F., additional, Ng, Lydia L., additional, Ng, Randy, additional, Orta, Geralyn J., additional, Overly, Caroline C., additional, Pak, Tu H., additional, Parry, Sheana E., additional, Pathak, Sayan D., additional, Pearson, Owen C., additional, Puchalski, Ralph B., additional, Riley, Zackery L., additional, Rockett, Hannah R., additional, Rowland, Stephen A., additional, Royall, Joshua J., additional, Ruiz, Marcos J., additional, Sarno, Nadia R., additional, Schaffnit, Katherine, additional, Shapovalova, Nadiya V., additional, Sivisay, Taz, additional, Slaughterbeck, Clifford R., additional, Smith, Simon C., additional, Smith, Kimberly A., additional, Smith, Bryan I., additional, Sodt, Andy J., additional, Stewart, Nick N., additional, Stumpf, Kenda-Ruth, additional, Sunkin, Susan M., additional, Sutram, Madhavi, additional, Tam, Angelene, additional, Teemer, Carey D., additional, Thaller, Christina, additional, Thompson, Carol L., additional, Varnam, Lee R., additional, Visel, Axel, additional, Whitlock, Ray M., additional, Wohnoutka, Paul E., additional, Wolkey, Crissa K., additional, Wong, Victoria Y., additional, Wood, Matthew, additional, Yaylaoglu, Murat B., additional, Young, Rob C., additional, Youngstrom, Brian L., additional, Feng Yuan, Xu, additional, Zhang, Bin, additional, Zwingman, Theresa A., additional, and Jones, Allan R., additional

Published
2006
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