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

Author: Yao, Zizhen, van Velthoven, Cindy T. J., Kunst, Michael, Zhang, Meng, McMillen, Delissa, Lee, Changkyu, Jung, Won, Goldy, Jeff, Abdelhak, Aliya, Aitken, Matthew, Baker, Katherine, Baker, Pamela, Barkan, Eliza, Bertagnolli, Darren, Bhandiwad, Ashwin, Bielstein, Cameron, Bishwakarma, Prajal, Campos, Jazmin, Carey, Daniel, Casper, Tamara, Chakka, Anish Bhaswanth, Chakrabarty, Rushil, Chavan, Sakshi, Chen, Min, Clark, Michael, Close, Jennie, Crichton, Kirsten, Daniel, Scott, DiValentin, Peter, Dolbeare, Tim, Ellingwood, Lauren, Fiabane, Elysha, Fliss, Timothy, Gee, James, Gerstenberger, James, Glandon, Alexandra, Gloe, Jessica, Gould, Joshua, Gray, James, Guilford, Nathan, Guzman, Junitta, Hirschstein, Daniel, Ho, Windy, Hooper, Marcus, Huang, Mike, Hupp, Madie, Jin, Kelly, Kroll, Matthew, Lathia, Kanan, Leon, Arielle, Li, Su, Long, Brian, Madigan, Zach, Malloy, Jessica, Malone, Jocelin, Maltzer, Zoe, Martin, Naomi, McCue, Rachel, McGinty, Ryan, Mei, Nicholas, Melchor, Jose, Meyerdierks, Emma, Mollenkopf, Tyler, Moonsman, Skyler, Nguyen, Thuc Nghi, Otto, Sven, Pham, Trangthanh, Rimorin, Christine, Ruiz, Augustin, Sanchez, Raymond, Sawyer, Lane, Shapovalova, Nadiya, Shepard, Noah, Slaughterbeck, Cliff, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Valera Cuevas, Nasmil, Vance, Shane, Wadhwani, Katherine, Ward, Katelyn, Levi, Boaz, Farrell, Colin, Young, Rob, Staats, Brian, Wang, Ming-Qiang Michael, Thompson, Carol L., Mufti, Shoaib, Pagan, Chelsea M., Kruse, Lauren, Dee, Nick, Sunkin, Susan M., Esposito, Luke, Hawrylycz, Michael J., Waters, Jack, Ng, Lydia, Smith, Kimberly, Tasic, Bosiljka, Zhuang, Xiaowei, and Zeng, Hongkui
Published: 2023
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2. Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons

Author: Dembrow, Nikolai C., Sawchuk, Scott, Dalley, Rachel, Opitz-Araya, Ximena, Hudson, Mark, Radaelli, Cristina, Alfiler, Lauren, Walling-Bell, Sarah, Bertagnolli, Darren, Goldy, Jeff, Johansen, Nelson, Miller, Jeremy A., Nasirova, Kamiliam, Owen, Scott F., Parga-Becerra, Alejandro, Taskin, Naz, Tieu, Michael, Vumbaco, David, Weed, Natalie, Wilson, Julia, Lee, Brian R., Smith, Kimberly A., Sorensen, Staci A., Spain, William J., Lein, Ed S., Perlmutter, Steve I., Ting, Jonathan T., and Kalmbach, Brian E.
Published: 2024
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3. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

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, and Mukamel, Eran A
Subjects: Human Genome, Neurosciences, Genetics, Bioengineering, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Atlases as Topic, Datasets as Topic, Epigenesis, Genetic, Epigenomics, Female, Gene Expression Profiling, Male, Mice, Motor Cortex, Neurons, Organ Specificity, Reproducibility of Results, Single-Cell Analysis, Transcriptome, General Science & Technology
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.
Published: 2021

4. 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

5. 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

6. 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

7. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

Author: Ben-Simon, Yoav, primary, Hooper, Marcus, additional, Narayan, Sujatha, additional, Daigle, Tanya, additional, Dwivedi, Deepanjali, additional, Way, Sharon W, additional, Oster, Aaron, additional, Stafford, David A, additional, Mich, John K, additional, Taormina, Michael J, additional, Martinez, Refugio A, additional, Opitz-Araya, Ximena, additional, Roth, Jada R, additional, Allen, Shona, additional, Ayala, Angela, additional, Bakken, Trygve E, additional, Barcelli, Tyler, additional, Barta, Stuard, additional, Bendrick, Jacqueline, additional, Bertagnolli, Darren, additional, Bowlus, Jessica, additional, Boyer, Gabriella, additional, Brouner, Krissy, additional, Casian, Brittny, additional, Casper, Tamara, additional, Chakka, Anish B, additional, Chakrabarty, Rushil, additional, Chance, Rebecca K, additional, Chavan, Sakshi, additional, Departee, Maxwell, additional, Donadio, Nicholas, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Gabitto, Mariano, additional, Gary, Amanda, additional, Gasperini, Molly, additional, Goldy, Jeff, additional, Gore, Bryan B, additional, Graybuck, Lucas, additional, Greisman, Noah, additional, Haeseleer, Francoise, additional, Halterman, Carliana, additional, Helback, Olivia, additional, Hockmeyer, Dirk, additional, Huang, Cindy, additional, Huff, Sydney, additional, Hunker, Avery, additional, Johansen, Nelson, additional, Juneau, Zoe, additional, Kalmbach, Brian, additional, Khem, Shannon, additional, Kutsal, Rana, additional, Larsen, Rachael, additional, Lee, Changkyu, additional, Lee, Angus Y, additional, Leibly, Madison, additional, Lenz, Garreck H, additional, Liang, Elizabeth, additional, Lusk, Nicholas, additional, Malone, Jocelin, additional, Mollenkopf, Tyler, additional, Morin, Elyse, additional, Newman, Dakota, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Omstead, Victoria, additional, Oyama, Alana, additional, Pham, Trangthanh, additional, Pom, Christina A, additional, Potekhina, Lydia, additional, Ransford, Shea, additional, Rette, Dean, additional, Rimorin, Christine, additional, Rocha, Dana, additional, Ruiz, Augustin, additional, Sanchez, Raymond E.A., additional, Sedeno-Cortes, Adriana, additional, Sevigny, Joshua P, additional, Shapovalova, Nadiya, additional, Shulga, Lyudmila, additional, Sigler, Ana R, additional, Siverts, La Akea, additional, Somasundaram, Saroja, additional, Stewart, Kaiya, additional, Tieu, Michael, additional, Trader, Cameron, additional, van Velthoven, Cindy T.J., additional, Walker, Miranda, additional, Weed, Natalie, additional, Wirthlin, Morgan, additional, Wood, Toren, additional, Wynalda, Brooke, additional, Yao, Zizhen, additional, Zhou, Thomas, additional, Ariza, Jeanelle, additional, Dee, Nick, additional, Reding, Melissa, additional, Ronellenfitch, Kara, additional, Mufti, Shoaib, additional, Sunkin, Susan M, additional, Smith, Kimberly A, additional, Esposito, Luke, additional, Waters, Jack, additional, Thyagarajan, Bargavi, additional, Yao, Shenqin, additional, Lein, Ed, additional, Zeng, Hongkui, additional, Levi, Boaz P, additional, Ngai, John, additional, Ting, Jonathan T, additional, and Tasic, Bosiljka, additional
Published: 2024
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8. Human neocortical expansion involves glutamatergic neuron diversification

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Published: 2021
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9. Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing

Author: Savage, Adam K., Gutschow, Miriam V., Chiang, Tony, Henderson, Kathy, Green, Richard, Chaudhari, Monica, Swanson, Elliott, Heubeck, Alexander T., Kondza, Nina, Burley, Kelli C., Genge, Palak C., Lord, Cara, Smith, Tanja, Thomson, Zachary, Beaubien, Aldan, Johnson, Ed, Goldy, Jeff, Bolouri, Hamid, Buckner, Jane H., Meijer, Paul, Coffey, Ernest M., Skene, Peter J., Torgerson, Troy R., Li, Xiao-jun, and Bumol, Thomas F.
Published: 2021
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10. 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

11. Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen

Author: Ting, Jonathan T., Johansen, Nelson J., Kalmbach, Brian E., Taskin, Naz, Lee, Brian, Clark, Jason K., Kendrick, Rennie, Ng, Lindsay, Radaelli, Cristina, Weed, Natalie, Enstrom, Rachel, Ransford, Shea, Redford, Ingrid, Walling-Bell, Sarah, Dalley, Rachel, Tieu, Michael, Goldy, Jeff, Jorstad, Nik, Smith, Kimberly, Bakken, Trygve, Lein, Ed S., and Owen, Scott F.
Published: 2024
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12. 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

13. Molecular hallmarks of Alzheimer’s disease with a multimodal single cell atlas of the cortex

Author: Travaglini, Kyle J, primary, Gabitto, Mariano I, additional, Ariza, Jeanelle, additional, Ding, Yi, additional, Mahoney, Joseph T, additional, Casper, Tamara, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Crane, Paul K, additional, Dee, Nick, additional, Ferrer, Rebecca, additional, Gatto, Nicole M, additional, Gloe, Jessica, additional, Goldy, Jeff, additional, Grabowski, Thomas J, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hawrylycz, Michael J, additional, Hodge, Rebecca D, additional, Jayadev, Suman, additional, Kaplan, Eitan S, additional, Keene, C Dirk, additional, Larson, Eric B, additional, Latimer, Caitlin S, additional, Levi, Boaz P, additional, Melief, Erica J, additional, Meyerdierks, Emma, additional, Mukherjee, Shubhabrata, additional, Pham, Thanh, additional, Rachleff, Victoria M, additional, Smith, Kimberly, additional, Torkelson, Amy, additional, Lein, Ed S, additional, and Miller, Jeremy A, additional
Published: 2023
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14. Multimodal and multiregional atlas of Alzheimer’s disease changes

Author: Gabitto, Mariano I, primary, Travaglini, Kyle J, additional, Ariza, Jeanelle, additional, Close, Jennie, additional, Ding, Yi, additional, Long, Brian, additional, Rachleff, Victoria M, additional, Chakrabarty, Rushil, additional, Crane, Paul K, additional, Ferrer, Rebecca, additional, Gatto, Nicole M, additional, Goldy, Jeff, additional, Grabowski, Thomas J, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hawrylycz, Michael J, additional, Hodge, Rebecca D, additional, Jayadev, Suman, additional, Kaplan, Eitan S, additional, Keene, C Dirk, additional, Larson, Eric B, additional, Latimer, Caitlin S, additional, Levi, Boaz P, additional, Mahoney, Joseph T, additional, Melief, Erica J, additional, Miller, Jeremy A, additional, Mukherjee, Shubhabrata, additional, Pham, Thanh, additional, Smith, Kimberly, additional, Torkelson, Amy, additional, Chakka, Anish Bhaswanth, additional, and Lein, Ed S, additional
Published: 2023
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15. Connecting single-cell transcriptomes to projectomes in mouse visual cortex

Author: Sorensen, Staci A., primary, Gouwens, Nathan W., additional, Wang, Yun, additional, Mallory, Matt, additional, Budzillo, Agata, additional, Dalley, Rachel, additional, Lee, Brian, additional, Gliko, Olga, additional, Kuo, Hsien-chi, additional, Kuang, Xiuli, additional, Mann, Rusty, additional, Ahmadinia, Leila, additional, Alfiler, Lauren, additional, Baftizadeh, Fahimeh, additional, Baker, Katherine, additional, Bannick, Sarah, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bohn, Phil, additional, Brown, Dillan, additional, Bomben, Jasmine, additional, Brouner, Krissy, additional, Chen, Chao, additional, Chen, Kai, additional, Chvilicek, Maggie, additional, Collman, Forrest, additional, Daigle, Tanya, additional, Dawes, Tim, additional, de Frates, Rebecca, additional, Dee, Nick, additional, DePartee, Maxwell, additional, Egdorf, Tom, additional, El-Hifnawi, Laila, additional, Enstrom, Rachel, additional, Esposito, Luke, additional, Farrell, Colin, additional, Gala, Rohan, additional, Glomb, Andrew, additional, Gamlin, Clare, additional, Gary, Amanda, additional, Goldy, Jeff, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hawrylycz, Mike, additional, Henry, Alex, additional, Hill, Dijon, additional, Hirokawa, Karla E., additional, Huang, Zili, additional, Johnson, Katelyn, additional, Juneau, Zoe, additional, Kebede, Sara, additional, Kim, Lisa, additional, Lee, Changkyu, additional, Lesnar, Phil, additional, Li, Anan, additional, Li, Yaoyao, additional, Liang, Elizabeth, additional, Link, Katie, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa A., additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ochoa, Thomas, additional, Oldre, Aaron, additional, Park, Daniel, additional, Pom, Christina Alice, additional, Popovich, Zoran, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ransford, Shea, additional, Reding, Melissa, additional, Ruiz, Augustin, additional, Sandman, David, additional, Siverts, La’Akea, additional, Smith, Kimberly A., additional, Stoecklin, Michelle, additional, Sulc, Josef, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, Dave, additional, Walker, Miranda, additional, Wang, Micheal, additional, Wanner, Adrian, additional, Waters, Jack, additional, Williams, Grace, additional, Wilson, Julia, additional, Xiong, Wei, additional, Lein, Ed, additional, Berg, Jim, additional, Kalmbach, Brian, additional, Yao, Shenqin, additional, Gong, Hui, additional, Luo, Qingming, additional, Ng, Lydia, additional, Sümbül, Uygar, additional, Jarsky, Tim, additional, Yao, Zizhen, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional
Published: 2023
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16. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex

Author: Lee, Brian R., primary, Dalley, Rachel, additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Close, Jennie, additional, Mann, Rusty, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bertagnolli, Darren, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva, additional, Donadio, Nicholas, additional, Driessens, Stan L.W., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A., additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, Dijon, additional, Hou, Wen-Hsien, additional, Johansen, Nelson, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, León, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J., additional, Molnar, Gabor, additional, Mortrud, Marty T., additional, Newman, Dakota, additional, Nyhus, Julie, additional, Opitz-Araya, Ximena, additional, Ozsvár, Attila, additional, Pham, Trangthanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ruiz, Augustin, additional, Sunkin, Susan M., additional, Szöts, Ildikó, additional, Taskin, Naz, additional, Thyagarajan, Bargavi, additional, Tieu, Michael, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Waleboer, Femke, additional, Walling-Bell, Sarah, additional, Weed, Natalie, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Shenqin, additional, Zhou, Thomas, additional, Barzó, Pál, additional, Bakken, Trygve, additional, Cobbs, Charles, additional, Dee, Nick, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W., additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Hodge, Rebecca, additional, Jarsky, Tim, additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Korshoej, Anders Rosendal, additional, Levi, Boaz P., additional, Meier, Kaare, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Sørensen, Jens Christian, additional, Waters, Jack, additional, Zeng, Hongkui, additional, Berg, Jim, additional, Capogna, Marco, additional, Goriounova, Natalia A., additional, Kalmbach, Brian, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D., additional, Sorensen, Staci A., additional, Tamas, Gabor, additional, Lein, Ed S., additional, and Ting, Jonathan T., additional
Published: 2023
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17. Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Author: Jorstad, Nikolas L., primary, Close, Jennie, additional, Johansen, Nelson, additional, Yanny, Anna Marie, additional, Barkan, Eliza R., additional, Travaglini, Kyle J., additional, Bertagnolli, Darren, additional, Campos, Jazmin, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hirschstein, Daniel, additional, Kiick, Katelyn, additional, Kroll, Matthew, additional, Kunst, Michael, additional, Lathia, Kanan, additional, Long, Brian, additional, Martin, Naomi, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Shapovalova, Nadiya, additional, Shehata, Soraya, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Callaway, Edward M., additional, Hof, Patrick R., additional, Keene, C. Dirk, additional, Levi, Boaz P., additional, Linnarsson, Sten, additional, Mitra, Partha P., additional, Smith, Kimberly, additional, Hodge, Rebecca D., additional, Bakken, Trygve E., additional, and Lein, Ed S, additional
Published: 2023
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18. Author Correction: 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, Preiss, 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., Ting, Jonathan T., Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R., Linnarsson, Sten, and Lein, Ed S.
Published: 2022
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19. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Published: 2022
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20. Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

Author: Mich, John K., primary, Sunil, Smrithi, additional, Johansen, Nelson, additional, Martinez, Refugio A., additional, Leytze, Mckaila, additional, Gore, Bryan B., additional, Mahoney, Joseph T., additional, Ben-Simon, Yoav, additional, Bishaw, Yemeserach, additional, Brouner, Krissy, additional, Campos, Jazmin, additional, Canfield, Ryan, additional, Casper, Tamara, additional, Dee, Nick, additional, Egdorf, Tom, additional, Gary, Amanda, additional, Gibson, Shane, additional, Goldy, Jeff, additional, Groce, Erin L., additional, Hirschstein, Daniel, additional, Loftus, Luke, additional, Lusk, Nick, additional, Malone, Jocelin, additional, Martin, Naomi X., additional, Monet, Deja, additional, Omstead, Victoria, additional, Opitz-Araya, Ximena, additional, Oster, Aaron, additional, Pom, Christina A., additional, Potekhina, Lydia, additional, Reding, Melissa, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Sedeño-Cortés, Adriana E., additional, Shapovalova, Nadiya V., additional, Taormina, Michael, additional, Taskin, Naz, additional, Tieu, Michael, additional, Valera Cuevas, Nasmil J., additional, Weed, Natalie, additional, Way, Sharon, additional, Yao, Zizhen, additional, McMillen, Delissa A., additional, Kunst, Michael, additional, McGraw, Medea, additional, Thyagarajan, Bargavi, additional, Waters, Jack, additional, Bakken, Trygve E., additional, Yao, Shenqin, additional, Smith, Kimberly A., additional, Svoboda, Karel, additional, Podgorski, Kaspar, additional, Kojima, Yoshiko, additional, Horwitz, Greg D., additional, Zeng, Hongkui, additional, Daigle, Tanya L., additional, Lein, Ed S., additional, Tasic, Bosiljka, additional, Ting, Jonathan T., additional, and Levi, Boaz P., additional
Published: 2023
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21. Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas

Author: Jin, Kelly, primary, Yao, Zizhen, additional, van Velthoven, Cindy T. J., additional, Kaplan, Eitan S., additional, Glattfelder, Katie, additional, Barlow, Samuel T., additional, Boyer, Gabriella, additional, Carey, Daniel, additional, Casper, Tamara, additional, Chakka, Anish Bhaswanth, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Departee, Max, additional, Desierto, Marie, additional, Gary, Amanda, additional, Gloe, Jessica, additional, Goldy, Jeff, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hirschstein, Daniel, additional, Lee, Changkyu, additional, Liang, Elizabeth, additional, Pham, Trangthanh, additional, Reding, Melissa, additional, Ronellenfitch, Kara, additional, Ruiz, Augustin, additional, Sevigny, Josh, additional, Shapovalova, Nadiya, additional, Shulga, Lyudmila, additional, Sulc, Josef, additional, Torkelson, Amy, additional, Tung, Herman, additional, Levi, Boaz, additional, Sunkin, Susan M., additional, Dee, Nick, additional, Esposito, Luke, additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional
Published: 2023
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22. Shared and distinct transcriptomic cell types across neocortical areas

Author: Tasic, Bosiljka, Yao, Zizhen, Graybuck, Lucas T., Smith, Kimberly A., Nguyen, Thuc Nghi, Bertagnolli, Darren, and Goldy, Jeff
Subjects: Brain cells -- Research, Neocortex -- Research, RNA sequencing -- Usage, Neurophysiology, GABA, Brain, Neurons, RNA, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA ([gamma]-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex. Single-cell transcriptomics of more than 20,000 cells from two functionally distinct areas of the mouse neocortex identifies 133 transcriptomic types, and provides a foundation for understanding the diversity of cortical cell types., Author(s): Bosiljka Tasic [sup.1] , Zizhen Yao [sup.1] , Lucas T. Graybuck [sup.1] , Kimberly A. Smith [sup.1] , Thuc Nghi Nguyen [sup.1] , Darren Bertagnolli [sup.1] , Jeff Goldy [...]
Published: 2018
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23. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano, primary, Travaglini, Kyle, additional, Ariza, Jeannelle, additional, Kaplan, Eitan, additional, Long, Brian, additional, Rachleff, Victoria, additional, Ding, Yi, additional, Mahoney, Joseph, additional, Dee, Nick, additional, Goldy, Jeff, additional, Melief, Erica, additional, Brouner, Krissy, additional, Compos, Jazmin, additional, Campos, John, additional, Carr, Ambrose, additional, Casper, Tamara, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Cool, Jonah, additional, Dalley, Rachel, additional, Darvas, Martin, additional, Dolbeare, Tim, additional, Ding, Song-Lin, additional, Egdorf, Tom, additional, Esposito, Luke, additional, Ferrer, Rebecca, additional, Gala, Rohan, additional, Gary, Amanda, additional, Gloe, Jessica, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Ho, Windy, additional, Jarsky, Tim, additional, Johansen, Nelson, additional, Kalmbach, Brian, additional, Keene, Lisa, additional, Khawand, Sarah, additional, Kilgore, Mitchell, additional, Kirkland, Amanda, additional, Kunst, Michael, additional, Lee, Brian, additional, Donald, Christine Mac, additional, Malone, Jocelin, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, McMillen, Delissa, additional, Meyerdierks, Emma, additional, Meyers, Kelly, additional, Mollenkopf, Tyler, additional, Montine, Mark, additional, Nolan, Amber, additional, Nyhus, Julie, additional, Olsen, Paul, additional, Pacleb, Maiya, additional, Pham, Trangthanh, additional, Pom, Christina, additional, Postupna, Nadia, additional, Ruiz, Augustin, additional, Schantz, Aimee, additional, Sorensen, Staci, additional, Staats, Brian, additional, Sullivan, Matt, additional, Sunkin, Susan, additional, Thompson, Carol, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Torkelson, Amy, additional, Tran, Tracy, additional, Cuevas, Nasmil Valera, additional, Wang, Ming-Qiang, additional, Waters, Jack, additional, Wilson, Angela, additional, Haynor, David, additional, Gatto, Nicole, additional, Jayadev, Suman, additional, Mufti, Shoaib, additional, Ng, Lydia, additional, Mukherjee, Shubhabrata, additional, Crane, Paul, additional, Latimer, Caitlin, additional, Levi, Boaz, additional, Smith, Kimberly, additional, Close, Jennie, additional, Miller, Jeremy, additional, Hodge, Rebecca, additional, Larson, Eric, additional, Grabowski, Thomas, additional, Hawrylycz, Michael, additional, Keene, C., additional, and Lein, Ed, additional
Published: 2023
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24. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano I., primary, Travaglini, Kyle J., additional, Rachleff, Victoria M., additional, Kaplan, Eitan S., additional, Long, Brian, additional, Ariza, Jeanelle, additional, Ding, Yi, additional, Mahoney, Joseph T., additional, Dee, Nick, additional, Goldy, Jeff, additional, Melief, Erica J., additional, Brouner, Krissy, additional, Campos, Jazmin, additional, Campos, John, additional, Carr, Ambrose J., additional, Casper, Tamara, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Cool, Jonah, additional, Valera Cuevas, Nasmil J., additional, Dalley, Rachel, additional, Darvas, Martin, additional, Ding, Song-Lin, additional, Dolbeare, Tim, additional, Mac Donald, Christine L., additional, Egdorf, Tom, additional, Esposito, Luke, additional, Ferrer, Rebecca, additional, Gala, Rohan, additional, Gary, Amanda, additional, Gloe, Jessica, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hirschstein, Daniel, additional, Ho, Windy, additional, Jarksy, Tim, additional, Johansen, Nelson, additional, Kalmbach, Brian E., additional, Keene, Lisa M., additional, Khawand, Sarah, additional, Kilgore, Mitch, additional, Kirkland, Amanda, additional, Kunst, Michael, additional, Lee, Brian R., additional, Malone, Jocelin, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, McMillen, Delissa, additional, Meyerdierks, Emma, additional, Meyers, Kelly P., additional, Mollenkopf, Tyler, additional, Montine, Mark, additional, Nolan, Amber L., additional, Nyhus, Julie, additional, Olsen, Paul A., additional, Pacleb, Maiya, additional, Peña, Nicholas, additional, Pham, Thanh, additional, Pom, Christina Alice, additional, Postupna, Nadia, additional, Ruiz, Augustin, additional, Schantz, Aimee M., additional, Shapovalova, Nadiya V., additional, Sorensen, Staci A., additional, Staats, Brian, additional, Sullivan, Matt, additional, Sunkin, Susan M., additional, Thompson, Carol, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Torkelson, Amy, additional, Tran, Tracy, additional, Wang, Ming-Qiang, additional, Waters, Jack, additional, Wilson, Angela M., additional, Haynor, David, additional, Gatto, Nicole, additional, Jayadev, Suman, additional, Mufti, Shoaib, additional, Ng, Lydia, additional, Mukherjee, Shubhabrata, additional, Crane, Paul K., additional, Latimer, Caitlin S., additional, Levi, Boaz P., additional, Smith, Kimberly, additional, Close, Jennie L., additional, Miller, Jeremy A., additional, Hodge, Rebecca D., additional, Larson, Eric B., additional, Grabowski, Thomas J., additional, Hawrylycz, Michael, additional, Dirk Keene, C., additional, and Lein, Ed S., additional
Published: 2023
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25. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Author: Chartrand, Thomas, Dalley, Rachel, Close, Jennie, Goriounova, Natalia A., Lee, Brian R., Mann, Rusty, Miller, Jeremy A., Molnar, Gabor, Mukora, Alice, Alfiler, Lauren, Baker, Katherine, Bakken, Trygve E., Berg, Jim, Bertagnolli, Darren, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Csajbok, Eva Adrienn, Dee, Nick, Egdorf, Tom, Enstrom, Rachel, Galakhova, Anna A., Gary, Amanda, Gelfand, Emily, Goldy, Jeff, Hadley, Kristen, Heistek, Tim S., Hill, Di Jon, Jorstad, Nik, Kim, Lisa, Kocsis, Agnes Katalin, Kruse, Lauren, Kunst, Michael, Leon, Gabriela, Long, Brian, Mallory, Matthew, McGraw, Medea, McMillen, Delissa, Melief, Erica J., Mihut, Norbert, Ng, Lindsay, Nyhus, Julie, Oláh, Gáspár, Ozsvár, Attila, Omstead, Victoria, Peterfi, Zoltan, Pom, Alice, Potekhina, Lydia, Rajanbabu, Ramkumar, Rozsa, Marton, Ruiz, Augustin, Sandle, Joanna, Sunkin, Susan M., Szots, Ildiko, Tieu, Michael, Toth, Martin, Trinh, Jessica, Vargas, Sara, Vumbaco, David, Williams, Grace, Wilson, Julia, Yao, Zizhen, Barzo, Pal, Cobbs, Charles, Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gouwens, Nathan W., Grannan, Benjamin, Gwinn, Ryder P., Hauptman, Jason S., Jarsky, Tim, Keene, C. Dirk, Ko, Andrew L., Koch, Christof, Ojemann, Jeffrey G., Patel, Anoop, Ruzevick, Jacob, Silbergeld, Daniel L., Smith, Kimberly, Sorensen, Staci A., Tasic, Bosiljka, Ting, Jonathan T., Waters, Jack, de Kock, Christiaan P.J., Mansvelder, Huib D., Tamas, Gabor, Zeng, Hongkui, Kalmbach, Brian, Lein, Ed S., Chartrand, Thomas, Dalley, Rachel, Close, Jennie, Goriounova, Natalia A., Lee, Brian R., Mann, Rusty, Miller, Jeremy A., Molnar, Gabor, Mukora, Alice, Alfiler, Lauren, Baker, Katherine, Bakken, Trygve E., Berg, Jim, Bertagnolli, Darren, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Csajbok, Eva Adrienn, Dee, Nick, Egdorf, Tom, Enstrom, Rachel, Galakhova, Anna A., Gary, Amanda, Gelfand, Emily, Goldy, Jeff, Hadley, Kristen, Heistek, Tim S., Hill, Di Jon, Jorstad, Nik, Kim, Lisa, Kocsis, Agnes Katalin, Kruse, Lauren, Kunst, Michael, Leon, Gabriela, Long, Brian, Mallory, Matthew, McGraw, Medea, McMillen, Delissa, Melief, Erica J., Mihut, Norbert, Ng, Lindsay, Nyhus, Julie, Oláh, Gáspár, Ozsvár, Attila, Omstead, Victoria, Peterfi, Zoltan, Pom, Alice, Potekhina, Lydia, Rajanbabu, Ramkumar, Rozsa, Marton, Ruiz, Augustin, Sandle, Joanna, Sunkin, Susan M., Szots, Ildiko, Tieu, Michael, Toth, Martin, Trinh, Jessica, Vargas, Sara, Vumbaco, David, Williams, Grace, Wilson, Julia, Yao, Zizhen, Barzo, Pal, Cobbs, Charles, Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gouwens, Nathan W., Grannan, Benjamin, Gwinn, Ryder P., Hauptman, Jason S., Jarsky, Tim, Keene, C. Dirk, Ko, Andrew L., Koch, Christof, Ojemann, Jeffrey G., Patel, Anoop, Ruzevick, Jacob, Silbergeld, Daniel L., Smith, Kimberly, Sorensen, Staci A., Tasic, Bosiljka, Ting, Jonathan T., Waters, Jack, de Kock, Christiaan P.J., Mansvelder, Huib D., Tamas, Gabor, Zeng, Hongkui, Kalmbach, Brian, and Lein, Ed S.
Abstract: Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neurons with extensive L1 branching, but whether L1 interneurons are similarly diverse is underexplored. Using Patch-seq recordings from human neurosurgical tissue, we identified four transcriptomic subclasses with mouse L1 homologs, along with distinct subtypes and types unmatched in mouse L1. Subclass and subtype comparisons showed stronger transcriptomic differences in human L1 and were correlated with strong morphoelectric variability along dimensions distinct from mouse L1 variability. Accompanied by greater layer thickness and other cytoarchitecture changes, these findings suggest that L1 has diverged in evolution, reflecting the demands of regulating the expanded human neocortical circuit.
Published: 2023
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26. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano I., Travaglini, Kyle J., Rachleff, Victoria M., Kaplan, Eitan S., Long, Brian, Ariza, Jeanelle, Ding, Yi, Mahoney, Joseph T., Dee, Nick, Goldy, Jeff, Melief, Erica J., Agrawal, Anamika, Kana, Omar, Zhen, Xingjian, Barlow, Samuel T., Brouner, Krissy, Campos, Jazmin, Campos, John, Carr, Ambrose J., Casper, Tamara, Chakrabarty, Rushil, Clark, Michael, Cool, Jonah, Dalley, Rachel, Darvas, Martin, Ding, Song-Lin, Dolbeare, Tim, Egdorf, Tom, Esposito, Luke, Ferrer, Rebecca, Fleckenstein, Lynn E., Gala, Rohan, Gary, Amanda, Gelfand, Emily, Gloe, Jessica, Guilford, Nathan, Guzman, Junitta, Hirschstein, Daniel, Ho, Windy, Hupp, Madison, Jarsky, Tim, Johansen, Nelson, Kalmbach, Brian E., Keene, Lisa M., Khawand, Sarah, Kilgore, Mitchell D., Kirkland, Amanda, Kunst, Michael, Lee, Brian R., Leytze, Mckaila, Mac Donald, Christine L., Malone, Jocelin, Maltzer, Zoe, Martin, Naomi, McCue, Rachel, McMillen, Delissa, Mena, Gonzalo, Meyerdierks, Emma, Meyers, Kelly P., Mollenkopf, Tyler, Montine, Mark, Nolan, Amber L., Nyhus, Julie K., Olsen, Paul A., Pacleb, Maiya, Pagan, Chelsea M., Peña, Nicholas, Pham, Trangthanh, Pom, Christina Alice, Postupna, Nadia, Rimorin, Christine, Ruiz, Augustin, Saldi, Giuseppe A., Schantz, Aimee M., Shapovalova, Nadiya V., Sorensen, Staci A., Staats, Brian, Sullivan, Matt, Sunkin, Susan M., Thompson, Carol, Tieu, Michael, Ting, Jonathan T., Torkelson, Amy, Tran, Tracy, Valera Cuevas, Nasmil J., Walling-Bell, Sarah, Wang, Ming-Qiang, Waters, Jack, Wilson, Angela M., Xiao, Ming, Haynor, David, Gatto, Nicole M., Jayadev, Suman, Mufti, Shoaib, Ng, Lydia, Mukherjee, Shubhabrata, Crane, Paul K., Latimer, Caitlin S., Levi, Boaz P., Smith, Kimberly A., Close, Jennie L., Miller, Jeremy A., Hodge, Rebecca D., Larson, Eric B., Grabowski, Thomas J., Hawrylycz, Michael, Keene, C. Dirk, and Lein, Ed S.
Abstract: Alzheimer’s disease (AD) is the leading cause of dementia in older adults. Although AD progression is characterized by stereotyped accumulation of proteinopathies, the affected cellular populations remain understudied. Here we use multiomics, spatial genomics and reference atlases from the BRAIN Initiative to study middle temporal gyrus cell types in 84 donors with varying AD pathologies. This cohort includes 33 male donors and 51 female donors, with an average age at time of death of 88 years. We used quantitative neuropathology to place donors along a disease pseudoprogression score. Pseudoprogression analysis revealed two disease phases: an early phase with a slow increase in pathology, presence of inflammatory microglia, reactive astrocytes, loss of somatostatin+inhibitory neurons, and a remyelination response by oligodendrocyte precursor cells; and a later phase with exponential increase in pathology, loss of excitatory neurons and Pvalb+and Vip+inhibitory neuron subtypes. These findings were replicated in other major AD studies.
Published: 2024
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27. 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, Baker, Pamela, additional, Barkan, Eliza, additional, Bertagnolli, Darren, 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, Dolbeare, Tim, additional, Ellingwood, Lauren, additional, Gee, 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, Jin, Kelly, additional, Kroll, Matthew, additional, Lathia, Kanan, additional, Leon, Arielle, additional, Long, Brian, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, Meyerdierks, Emma, additional, Nguyen, Thuc Nghi, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Shapovalova, Nadiya, additional, Slaughterbeck, Cliff, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Cuevas, Nasmil Valera, additional, Wadhwani, Katherine, additional, Ward, Katelyn, additional, Levi, Boaz, additional, Farrell, Colin, 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 A., additional, Tasic, Bosiljka, additional, Zhuang, Xiaowei, additional, and Zeng, Hongkui, additional
Published: 2023
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28. A multimodal atlas of the molecular and cellular changes to cortex driven by Alzheimer’s disease

Author: Travaglini, Kyle J, primary, Gabitto, Mariano, additional, Ding, Yi, additional, Ariza, Jeanelle, additional, Chakrabarty, Rushil, additional, Crane, Paul K., additional, Ferrer, Rebecca, additional, Goldy, Jeff, additional, Grabowski, Thomas J, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hawrylycz, Michael J, additional, Hodge, Rebecca D, additional, Jayadev, Suman, additional, Kaplan, Eitan S, additional, Keene, C Dirk, additional, Larson, Eric B, additional, Latimer, Caitlin S, additional, Levi, Boaz, additional, Mahoney, Joseph, additional, Melief, Erica J, additional, Mukherjee, Shubhabrata, additional, Pham, Thanh, additional, Rachleff, Victoria M, additional, Smith, Kimberly A, additional, Torkelson, Amy, additional, Lein, Ed S, additional, and Miller, Jeremy A, additional
Published: 2022
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29. Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

Author: Lee, Brian, primary, Dalley, Rachel, additional, Miller, Jeremy A, additional, Chartrand, Thomas, additional, Close, Jennie, additional, Mann, Rusty, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bertagnolli, Darren, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva, additional, Dee, Nick, additional, Donadio, Nicholas, additional, Driessens, Stan L.W., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, Dijon, additional, Johansen, Nelson, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, Leon, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J, additional, Molnar, Gabor, additional, Mortrud, Marty T, additional, Newman, Dakota, additional, Nyhus, Julie, additional, Opitz-Araya, Ximena, additional, Pham, Trangthanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ruiz, Augustin, additional, Sunkin, Susan M, additional, Szots, Ildiko, additional, Taskin, Naz, additional, Thyagarajan, Bargavi, additional, Tieu, Michael, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Waleboer, Femke, additional, Weed, Natalie, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Shenqin, additional, Zhou, Thomas, additional, Barzo, Pal, additional, Bakken, Trygve, additional, Cobbs, Charles, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W, additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Hodge, Rebecca, additional, Jarsky, Tim, additional, Keene, C.Dirk, additional, Ko, Andrew L., additional, Levi, Boaz, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silbergeld, Daniel L., additional, Smith, Kim, additional, Waters, Jack, additional, Zeng, Hongkui, additional, Berg, Jim, additional, Goriounova, Natalia A., additional, Kalmbach, Brian, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D, additional, Sorensen, Staci A, additional, Tamas, Gabor, additional, Lein, Ed S., additional, and Ting, Jonathan T, additional
Published: 2022
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30. Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Author: Jorstad, Nikolas L., primary, Close, Jennie, additional, Johansen, Nelson, additional, Yanny, Anna Marie, additional, Barkan, Eliza R., additional, Travaglini, Kyle J., additional, Bertagnolli, Darren, additional, Campos, Jazmin, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hirschstein, Daniel, additional, Kroll, Matthew, additional, Kunst, Michael, additional, Lathia, Kanan, additional, Long, Brian, additional, Martin, Naomi, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Shapovalova, Nadiya, additional, Shehata, Soraya, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Ward, Katelyn, additional, Callaway, Edward M., additional, Hof, Patrick R., additional, Keene, C. Dirk, additional, Levi, Boaz P., additional, Linnarsson, Sten, additional, Mitra, Partha P., additional, Smith, Kimberly, additional, Hodge, Rebecca D., additional, Bakken, Trygve E., additional, and Lein, Ed S., additional
Published: 2022
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31. Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Author: Chartrand, Thomas, primary, Dalley, Rachel, additional, Close, Jennie, additional, Goriounova, Natalia A., additional, Lee, Brian R., additional, Mann, Rusty, additional, Miller, Jeremy A., additional, Molnar, Gabor, additional, Mukora, Alice, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bakken, Trygve E., additional, Berg, Jim, additional, Bertagnolli, Darren, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva Adrienn, additional, Dee, Nick, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A., additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, DiJon, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, Leon, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J., additional, Mihut, Norbert, additional, Ng, Lindsay, additional, Nyhus, Julie, additional, Omstead, Victoria, additional, Peterfi, Zoltan, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Rozsa, Marton, additional, Ruiz, Augustin, additional, Sandle, Joanna, additional, Sunkin, Susan M., additional, Szots, Ildiko, additional, Tieu, Michael, additional, Toth, Martin, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Zizhen, additional, Barzo, Pal, additional, Cobbs, Charles, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W., additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Jarsky, Tim, additional, Keene, C.Dirk, additional, Ko, Andrew L., additional, Koch, Christof, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silberberg, Daniel L., additional, Smith, Kimberly, additional, Sorensen, Staci A., additional, Tasic, Bosiljka, additional, Ting, Jonathan T., additional, Waters, Jack, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D., additional, Tamas, Gabor, additional, Zeng, Hongkui, additional, Kalmbach, Brian, additional, and Lein, Ed S., additional
Published: 2022
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32. Inter-individual variation in human cortical cell type abundance and expression

Author: Johansen, Nelson, primary, Somasundaram, Saroja, additional, Travaglini, Kyle J., additional, Yanny, Anna Marie, additional, Shumyatcher, Maya, additional, Casper, Tamara, additional, Cobbs, Charles, additional, Dee, Nick, additional, Ellenbogen, Richard, additional, Ferreira, Manuel, additional, Goldy, Jeff, additional, Guzman, Junitta, additional, Gwinn, Ryder, additional, Hirschstein, Daniel, additional, Jorstad, Nikolas L., additional, Keene, C. Dirk, additional, Ko, Andrew, additional, Levi, Boaz P., additional, Ojemann, Jeffrey G., additional, Pham, Thanh, additional, Shapovalova, Nadiya, additional, Silbergeld, Daniel, additional, Sulc, Josef, additional, Torkelson, Amy, additional, Tung, Herman, additional, Smith, Kimberly, additional, Lein, Ed S., additional, Bakken, Trygve E., additional, Hodge, Rebecca D., additional, and Miller, Jeremy A., additional
Published: 2022
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33. Comparative transcriptomics reveals human-specific cortical features

Author: Jorstad, Nikolas L., primary, Song, Janet H.T., additional, Exposito-Alonso, David, additional, Suresh, Hamsini, additional, Castro, Nathan, additional, Krienen, Fenna M., additional, Yanny, Anna Marie, additional, Close, Jennie, additional, Gelfand, Emily, additional, Travaglini, Kyle J., additional, Basu, Soumyadeep, additional, Beaudin, Marc, additional, Bertagnolli, Darren, additional, Crow, Megan, additional, Ding, Song-Lin, additional, Eggermont, Jeroen, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Kroes, Thomas, additional, Long, Brian, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Ward, Katelyn, additional, Feng, Guoping, additional, Hopkins, William D., additional, Höllt, Thomas, additional, Keene, C. Dirk, additional, Linnarsson, Sten, additional, McCarroll, Steven A., additional, Lelieveldt, Boudewijn P., additional, Sherwood, Chet C., additional, Smith, Kimberly, additional, Walsh, Christopher A., additional, Dobin, Alexander, additional, Gillis, Jesse, additional, Lein, Ed S., additional, Hodge, Rebecca D., additional, and Bakken, Trygve E., additional
Published: 2022
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34. 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., Ting, Jonathan T., Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R., Linnarsson, Sten, Lein, Ed S., 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., Ting, Jonathan T., Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R., Linnarsson, Sten, and Lein, Ed S.
Abstract: AbstractThe 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: 2022

35. Author Correction:Human neocortical expansion involves glutamatergic neuron diversification (Nature, (2021), 598, 7879, (151-158), 10.1038/s41586-021-03813-8)

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Abstract: In the version of this Article initially published, the Acknowledgements statement contained an error. Originally appearing with thanks for support given in part as follows, “R01EY023173 from The National Eye Institute, U01MH105982 from the National Institute of Mental Health and Eunice Kennedy Shriver National Institute of Child Health and Human Development, and R011EY023173 from The National Institute of Allergy and Infectious Disease,” the last number (R011EY023173) was mistakenly added and is not in fact a grant or one provided by the NIAID. The mention has been removed. The changes have been made to the online version of the Article.
Published: 2022
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36. Divergent and nonuniform gene expression patterns in mouse brain

Author: Morris, John A., Royall, Joshua J., Bertagnolli, Darren, Boe, Andrew F., Burnell, Josh J., Byrnes, Emi J., Copeland, Cathy, Desta, Tsega, Fischer, Shanna R., Goldy, Jeff, Glattfelder, Katie J., Kidney, Jolene M., Lemon, Tracy, Orta, Geralyn J., Parry, Sheana E., Pathak, Sayan D., Pearson, Owen C., Reding, Melissa, Shapouri, Sheila, Smith, Kimberly A., Soden, Chad, Solan, Beth M., Weller, John, Takahashi, Joseph S., Overly, Caroline C., Lein, Ed S., Hawrylycz, Michael J., Hohmann, John G., Jones, Allan R., and Jones, Edward G.
Published: 2010

37. Local connectivity and synaptic dynamics in mouse and human neocortex

Author: Campagnola, Luke, primary, Seeman, Stephanie C., additional, Chartrand, Thomas, additional, Kim, Lisa, additional, Hoggarth, Alex, additional, Gamlin, Clare, additional, Ito, Shinya, additional, Trinh, Jessica, additional, Davoudian, Pasha, additional, Radaelli, Cristina, additional, Kim, Mean-Hwan, additional, Hage, Travis, additional, Braun, Thomas, additional, Alfiler, Lauren, additional, Andrade, Julia, additional, Bohn, Phillip, additional, Dalley, Rachel, additional, Henry, Alex, additional, Kebede, Sara, additional, Alice, Mukora, additional, Sandman, David, additional, Williams, Grace, additional, Larsen, Rachael, additional, Teeter, Corinne, additional, Daigle, Tanya L., additional, Berry, Kyla, additional, Dotson, Nadia, additional, Enstrom, Rachel, additional, Gorham, Melissa, additional, Hupp, Madie, additional, Dingman Lee, Samuel, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Potekhina, Lydia, additional, Ransford, Shea, additional, Gary, Amanda, additional, Goldy, Jeff, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Tieu, Michael, additional, Siverts, La’Akea, additional, Walker, Miranda, additional, Farrell, Colin, additional, Schroedter, Martin, additional, Slaughterbeck, Cliff, additional, Cobb, Charles, additional, Ellenbogen, Richard, additional, Gwinn, Ryder P., additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Ojemann, Jeffrey G., additional, Silbergeld, Daniel L., additional, Carey, Daniel, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Clark, Michael, additional, Dee, Nick, additional, Ellingwood, Lauren, additional, Gloe, Jessica, additional, Kroll, Matthew, additional, Sulc, Josef, additional, Tung, Herman, additional, Wadhwani, Katherine, additional, Brouner, Krissy, additional, Egdorf, Tom, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, Pom, Christina Alice, additional, Ruiz, Augustin, additional, Bomben, Jasmine, additional, Feng, David, additional, Hejazinia, Nika, additional, Shi, Shu, additional, Szafer, Aaron, additional, Wakeman, Wayne, additional, Phillips, John, additional, Bernard, Amy, additional, Esposito, Luke, additional, D’Orazi, Florence D., additional, Sunkin, Susan, additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Arkhipov, Anton, additional, Sorensen, Staci, additional, Lein, Ed, additional, Koch, Christof, additional, Murphy, Gabe, additional, Zeng, Hongkui, additional, and Jarsky, Tim, additional
Published: 2022
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38. 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 T. J., Vanderburg, Charles R., Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D., Osteen, Julia K., Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Wang, Xinxin, Aldridge, Andrew I., Bartlett, Anna, Boggeman, Lara, O’Connor, Carolyn, Castanon, Rosa G., Chen, Huaming, Fitzpatrick, Conor, Luo, Chongyuan, Nery, Joseph R., Nunn, Michael, Rivkin, Angeline C., Tian, Wei, Dominguez, Bertha, Ito-Cole, Tony, Jacobs, Matthew, Jin, Xin, Lee, Cheng-Ta, Lee, Kuo-Fen, Miyazaki, Paula Assakura, Pang, Yan, Rashid, Mohammad, Smith, Jared B., Vu, Minh, Williams, Elora, Biancalani, Tommaso, Booeshaghi, A. Sina, Crow, Megan, Dudoit, Sandrine, Fischer, Stephan, Gillis, Jesse, Hu, Qiwen, Kharchenko, Peter V., Niu, Sheng-Yong, Ntranos, Vasilis, Purdom, Elizabeth, Risso, Davide, de Bézieux, Hector Roux, Somasundaram, Saroja, Street, Kelly, Svensson, Valentine, Vaishnav, Eeshit Dhaval, Van den Berge, Koen, Welch, Joshua D., An, Xu, Bateup, Helen S., Bowman, Ian, Chance, Rebecca K., Foster, Nicholas N., Galbavy, William, Gong, Hui, Gou, Lin, Hatfield, Joshua T., Hintiryan, Houri, Hirokawa, Karla E., Kim, Gukhan, Kramer, Daniel J., Li, Anan, Li, Xiangning, Luo, Qingming, Muñoz-Castañeda, Rodrigo, Stafford, David A., Feng, Zhao, Jia, Xueyan, Jiang, Shengdian, Jiang, Tao, Kuang, Xiuli, Larsen, Rachael, Lesnar, Phil, Li, Yaoyao, Li, Yuanyuan, Liu, Lijuan, Peng, Hanchuan, Qu, Lei, Ren, Miao, Ruan, Zongcai, Shen, Elise, Song, Yuanyuan, Wakeman, Wayne, Wang, Peng, Wang, Yimin, Wang, Yun, Yin, Lulu, Yuan, Jing, Zhao, Sujun, Zhao, Xuan, Narasimhan, Arun, Palaniswamy, Ramesh, Banerjee, Samik, Ding, Liya, Huilgol, Dhananjay, Huo, Bingxing, Kuo, Hsien-Chi, Laturnus, Sophie, Li, Xu, Mitra, Partha P., Mizrachi, Judith, Wang, Quanxin, Xie, Peng, Xiong, Feng, Yu, Yang, Eichhorn, Stephen W., Berg, Jim, Bernabucci, Matteo, Bernaerts, Yves, Cadwell, Cathryn René, Castro, Jesus Ramon, Dalley, Rachel, Hartmanis, Leonard, Horwitz, Gregory D., Jiang, Xiaolong, Ko, Andrew L., Miranda, Elanine, Mulherkar, Shalaka, Nicovich, Philip R., Owen, Scott F., Sandberg, Rickard, Sorensen, Staci A., Tan, Zheng Huan, Allen, Shona, Hockemeyer, Dirk, Lee, Angus Y., Veldman, Matthew B., Adkins, Ricky S., Ament, Seth A., Bravo, Héctor Corrada, Carter, Robert, Chatterjee, Apaala, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Felix, Victor, Giglio, Michelle, Herb, Brian R., Kancherla, Jayaram, Mahurkar, Anup, McCracken, Carrie, Nickel, Lance, Olley, Dustin, Orvis, Joshua, Schor, Michael, Hood, Greg, Dichter, Benjamin, Grauer, Michael, Helba, Brian, Bandrowski, Anita, Barkas, Nikolaos, Carlin, Benjamin, D’Orazi, Florence D., Degatano, Kylee, Gillespie, Thomas H., Khajouei, Farzaneh, Konwar, Kishori, Thompson, Carol, Kelly, Kathleen, Mok, Stephanie, Sunkin, Susan, BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, [missing], BICCN contributing principal investigators, [missing], Principal manuscript editors, [missing], Manuscript writing and figure generation, [missing], Analysis coordination, [missing], Integrated data analysis, [missing], scRNA-seq and snRNA-seq data generation and processing, [missing], ATAC-seq data generation and processing, [missing], Methylcytosine data production and analysis, [missing], Epi-retro-seq data generation and processing, [missing], ‘Omics data analysis, [missing], Tracing and connectivity data generation, [missing], Morphology data generation and reconstruction, [missing], OLST/STPT and other data generation, [missing], Morphology, connectivity and imaging analysis, [missing], Spatially resolved single-cell transcriptomics (MERFISH), [missing], Multimodal profiling (Patch-seq), [missing], Transgenic tools, [missing], NeMO archive and analytics, [missing], Brain Image Library (BIL) archive, [missing], DANDI archive, [missing], Brain Cell Data Center (BCDC), [missing], Project management, [missing], and BRAIN Initiative Cell Census Network (BICCN), [missing]
Subjects: Epigenomics, Male, INTERNEURONS, ORGANIZATION, MOUSE, Molecular neuroscience, Neural circuits, CLASSIFICATION, Article, Mice, Atlases as Topic, Glutamates, Species Specificity, Animals, Humans, TRANSCRIPTOMICS, SPECIFICATION, NEURONS, In Situ Hybridization, Fluorescence, Phylogeny, Neurons, Multidisciplinary, Gene Expression Profiling, Biology and Life Sciences, PATHWAYS, Brain, Callithrix, Censuses, Cellular neuroscience, Mathematics and Statistics, SINGLE, Organ Specificity, MORPHOLOGY, Motor cortex, Female, Single-Cell Analysis, Transcriptome
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., The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.
Published: 2021

39. Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

Author: Bakken, Trygve E, primary, van Velthoven, Cindy TJ, additional, Menon, Vilas, additional, Hodge, Rebecca D, additional, Yao, Zizhen, additional, Nguyen, Thuc Nghi, additional, Graybuck, Lucas T, additional, Horwitz, Gregory D, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Yanny, Anna Marie, additional, Garren, Emma, additional, Parry, Sheana, additional, Casper, Tamara, additional, Shehata, Soraya I, additional, Barkan, Eliza R, additional, Szafer, Aaron, additional, Levi, Boaz P, additional, Dee, Nick, additional, Smith, Kimberly A, additional, Sunkin, Susan M, additional, Bernard, Amy, additional, Phillips, John, additional, Hawrylycz, Michael J, additional, Koch, Christof, additional, Murphy, Gabe J, additional, Lein, Ed, additional, Zeng, Hongkui, additional, and Tasic, Bosiljka, additional
Published: 2021
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40. INTER-INDIVIDUAL VARIATION IN HUMAN CORTICAL CELL TYPE ABUNDANCE AND EXPRESSION

Author: Johansen, Nelson, Somasundaram, Saroja, Travaglini, Kyle, Yanny, Anna Marie, Shumyatcher, Maya, Casper, Tamara, Cobbs, Charles, Dee, Nick, Ellenbogen, Richard, Ferreira, Manuel, Goldy, Jeff, Guzman, Junitta, Gwinn, Ryder, Hirschstein, Daniel, Jorstad, Nikolas, Keene, C. Dirk, Ko, Andrew, Levi, Boaz, Ojemann, Jeffrey, Pham, Thanh, Shapovalova, Nadiya, Silbergeld, Daniel, Sulc, Josef, Torkelson, Amy, Tung, Herman, Smith, Kimberly, Lein, Ed, Bakken, Trygve, Hodge, Rebecca, and Miller, Jeremy
Published: 2023
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41. Author response: Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

Author: Bakken, Trygve E, primary, van Velthoven, Cindy TJ, additional, Menon, Vilas, additional, Hodge, Rebecca D, additional, Yao, Zizhen, additional, Nguyen, Thuc Nghi, additional, Graybuck, Lucas T, additional, Horwitz, Gregory D, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Yanny, Anna Marie, additional, Garren, Emma, additional, Parry, Sheana, additional, Casper, Tamara, additional, Shehata, Soraya I, additional, Barkan, Eliza R, additional, Szafer, Aaron, additional, Levi, Boaz P, additional, Dee, Nick, additional, Smith, Kimberly A, additional, Sunkin, Susan M, additional, Bernard, Amy, additional, Phillips, John, additional, Hawrylycz, Michael J, additional, Koch, Christof, additional, Murphy, Gabe J, additional, Lein, Ed, additional, Zeng, Hongkui, additional, and Tasic, Bosiljka, additional
Published: 2021
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42. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Author: Yao, Zizhen, primary, van Velthoven, Cindy T.J., additional, Nguyen, Thuc Nghi, additional, Goldy, Jeff, additional, Sedeno-Cortes, Adriana E., additional, Baftizadeh, Fahimeh, additional, Bertagnolli, Darren, additional, Casper, Tamara, additional, Chiang, Megan, additional, Crichton, Kirsten, additional, Ding, Song-Lin, additional, Fong, Olivia, additional, Garren, Emma, additional, Glandon, Alexandra, additional, Gouwens, Nathan W., additional, Gray, James, additional, Graybuck, Lucas T., additional, Hawrylycz, Michael J., additional, Hirschstein, Daniel, additional, Kroll, Matthew, additional, Lathia, Kanan, additional, Lee, Changkyu, additional, Levi, Boaz, additional, McMillen, Delissa, additional, Mok, Stephanie, additional, Pham, Thanh, additional, Ren, Qingzhong, additional, Rimorin, Christine, additional, Shapovalova, Nadiya, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Ward, Katelyn, additional, Dee, Nick, additional, Smith, Kimberly A., additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional
Published: 2021
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43. Enhancer viruses for combinatorial cell-subclass-specific labeling

Author: Graybuck, Lucas T., primary, Daigle, Tanya L., additional, Sedeño-Cortés, Adriana E., additional, Walker, Miranda, additional, Kalmbach, Brian, additional, Lenz, Garreck H., additional, Morin, Elyse, additional, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, Bendrick, Jacqueline L., additional, Kim, Tae Kyung, additional, Zhou, Thomas, additional, Mortrud, Marty, additional, Yao, Shenqin, additional, Siverts, La’ Akea, additional, Larsen, Rachael, additional, Gore, Bryan B., additional, Szelenyi, Eric R., additional, Trader, Cameron, additional, Balaram, Pooja, additional, van Velthoven, Cindy T.J., additional, Chiang, Megan, additional, Mich, John K., additional, Dee, Nick, additional, Goldy, Jeff, additional, Cetin, Ali H., additional, Smith, Kimberly, additional, Way, Sharon W., additional, Esposito, Luke, additional, Yao, Zizhen, additional, Gradinaru, Viviana, additional, Sunkin, Susan M., additional, Lein, Ed, additional, Levi, Boaz P., additional, Ting, Jonathan T., additional, Zeng, Hongkui, additional, and Tasic, Bosiljka, additional
Published: 2021
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44. Local Connectivity and Synaptic Dynamics in Mouse and Human Neocortex

Author: Campagnola, Luke, primary, Seeman, Stephanie C, additional, Chartrand, Thomas, additional, Kim, Lisa, additional, Hoggarth, Alex, additional, Gamlin, Clare, additional, Ito, Shinya, additional, Trinh, Jessica, additional, Davoudian, Pasha, additional, Radaelli, Cristina, additional, Kim, Mean-Hwan, additional, Hage, Travis, additional, Braun, Thomas, additional, Alfiler, Lauren, additional, Andrade, Juia, additional, Bohn, Phillip, additional, Dalley, Rachel, additional, Henry, Alex, additional, Kebede, Sara, additional, Mukora, Alice, additional, Sandman, David, additional, Williams, Grace, additional, Larsen, Rachael, additional, Teeter, Corinne, additional, Daigle, Tanya L., additional, Berry, Kyla, additional, Dotson, Nadia, additional, Enstrom, Rachel, additional, Gorham, Melissa, additional, Hupp, Madie, additional, Lee, Samuel Dingman, additional, Ngo, Kiet, additional, Nicovich, Rusty, additional, Potekhina, Lydia, additional, Ransford, Shea, additional, Gary, Amanda, additional, Goldy, Jeff, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Tieu, Michael, additional, Siverts, La’Akea, additional, Walker, Miranda, additional, Farrell, Colin, additional, Schroedter, Martin, additional, Slaughterbeck, Cliff, additional, Cobb, Charles, additional, Ellenbogen, Richard, additional, Gwinn, Ryder P, additional, Keene, C. Dirk, additional, Ko, Andrew L, additional, Ojemann, Jeffrey G, additional, Silbergeld, Daniel L, additional, Carey, Daniel, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Clark, Michael, additional, Dee, Nick, additional, Ellingwood, Lauren, additional, Gloe, Jessica, additional, Kroll, Matthew, additional, Sulc, Josef, additional, Tung, Herman, additional, Wadhwani, Katherine, additional, Brouner, Krissy, additional, Egdorf, Tom, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, Pom, Christina Alice, additional, Ruiz, Augustin, additional, Bomben, Jasmine, additional, Feng, David, additional, Hejazinia, Nika, additional, Shi, Shu, additional, Szafer, Aaron, additional, Wakeman, Wayne, additional, Phillips, John, additional, Bernard, Amy, additional, Esposito, Luke, additional, D’Orazi, Florence D, additional, Sunkin, Susan, additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Arkhipov, Anton, additional, Sorensen, Staci, additional, Lein, Ed, additional, Koch, Christof, additional, Murphy, Gabe, additional, Zeng, Hongkui, additional, and Jarsky, Tim, additional
Published: 2021
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45. 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 GuigÃ³ (corresponding author) [4, 5]; Thomas [...]
Published: 2007
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46. An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Author: Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S., Aldrige, Andrew I., Ament, Seth A., Bartlett, Ann, Behrens, M. Margarita, Van den Berge, Koen, Bertagnolli, Darren, Biancalani, Tommaso, Booeshaghi, A. Sina, Corrada Bravo, Hector, 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, Michael, Roux de Bezieux, Hector, Herb, Brian R., Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Huang, Z. Josh, 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, Gillis, Jesse, Kharchenko, Peter V., Ngai, John, Pachter, Lior, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D., Ecker, Joseph R., Macosko, Evan, Ren, Bing, Zeng, Hongkui, Mukamel, Eran A., Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S., Aldrige, Andrew I., Ament, Seth A., Bartlett, Ann, Behrens, M. Margarita, Van den Berge, Koen, Bertagnolli, Darren, Biancalani, Tommaso, Booeshaghi, A. Sina, Corrada Bravo, Hector, 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, Michael, Roux de Bezieux, Hector, Herb, Brian R., Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Huang, Z. Josh, 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, Gillis, Jesse, Kharchenko, Peter V., Ngai, John, Pachter, Lior, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D., Ecker, Joseph R., Macosko, Evan, Ren, Bing, Zeng, Hongkui, and Mukamel, Eran A.
Abstract: Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful cell types. We used a battery of single-cell transcriptome and epigenome measurements generated by the BRAIN Initiative Cell Census Network (BICCN) to comprehensively assess the molecular signatures of cell types in the mouse primary motor cortex (MOp). We further developed computational and statistical methods to integrate these multimodal data and quantitatively validate the reproducibility of the cell types. The reference atlas, based on more than 600,000 high quality single-cell or -nucleus samples assayed by six molecular modalities, is a comprehensive molecular account of the diverse neuronal and non-neuronal cell types in MOp. Collectively, our study indicates that the mouse primary motor cortex contains over 55 neuronal cell types that are highly replicable across analysis methods, sequencing technologies, and modalities. We find many concordant multimodal markers for each cell type, as well as thousands of genes and gene regulatory elements with discrepant transcriptomic and epigenomic signatures. These data highlight the complex molecular regulation of brain cell types and will directly enable design of reagents to target specific MOp cell types for functional analysis.
Published: 2020

47. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Author: Mich, John K., primary, Graybuck, Lucas T., additional, Hess, Erik E., additional, Mahoney, Joseph T., additional, Kojima, Yoshiko, additional, Ding, Yi, additional, Somasundaram, Saroja, additional, Miller, Jeremy A., additional, Kalmbach, Brian E., additional, Radaelli, Cristina, additional, Gore, Bryan B., additional, Weed, Natalie, additional, Omstead, Victoria, additional, Bishaw, Yemeserach, additional, Shapovalova, Nadiya V., additional, Martinez, Refugio A., additional, Fong, Olivia, additional, Yao, Shenqin, additional, Mortrud, Marty, additional, Chong, Peter, additional, Loftus, Luke, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Casper, Tamara, additional, Dee, Nick, additional, Opitz-Araya, Ximena, additional, Cetin, Ali, additional, Smith, Kimberly A., additional, Gwinn, Ryder P., additional, Cobbs, Charles, additional, Ko, Andrew L., additional, Ojemann, Jeffrey G., additional, Keene, C. Dirk, additional, Silbergeld, Daniel L., additional, Sunkin, Susan M., additional, Gradinaru, Viviana, additional, Horwitz, Gregory D., additional, Zeng, Hongkui, additional, Tasic, Bosiljka, additional, Lein, Ed S., additional, Ting, Jonathan T., additional, and Levi, Boaz P., additional
Published: 2021
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48. Mapping of Charcot-Marie-Tooth disease type 1C to chromosome 16p identifies a novel locus for demyelinating neuropathies. (Report)

Author: Street, Valerie A., Goldy, Jeff D., Golden, Alana S., Tempel, Bruce L, Bird, Thomas D., and Chance, Phillip F.
Subjects: Charcot-Marie-Tooth disease -- Genetic aspects, Peripheral nerve diseases -- Genetic aspects, Genetic disorders -- Research, Biological sciences
Published: 2002

49. 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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50. Single-cell RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates and humans

Author: Bakken, Trygve E., primary, van Velthoven, Cindy T.J., additional, Menon, Vilas, additional, Hodge, Rebecca D., additional, Yao, Zizhen, additional, Nguyen, Thuc Nghi, additional, Graybuck, Lucas T., additional, Horwitz, Gregory D., additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Garren, Emma, additional, Parry, Sheana, additional, Casper, Tamara, additional, Shehata, Soraya I., additional, Barkan, Eliza R., additional, Szafer, Aaron, additional, Levi, Boaz P., additional, Dee, Nick, additional, Smith, Kimberly A., additional, Sunkin, Susan M., additional, Bernard, Amy, additional, Phillips, John W., additional, Hawrylycz, Michael, additional, Koch, Christof, additional, Murphy, Gabe, additional, Lein, Ed, additional, Zeng, Hongkui, additional, and Tasic, Bosiljka, additional
Published: 2020
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