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1. 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

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

Author

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

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

Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

Published
2021

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

Author

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

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

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

Published
2019

4. 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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5. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Author

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

Published
2021
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6. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Author

Mich, John K., Graybuck, Lucas T., Hess, Erik E., Mahoney, Joseph T., Kojima, Yoshiko, Ding, Yi, Somasundaram, Saroja, Miller, Jeremy A., Kalmbach, Brian E., Radaelli, Cristina, Gore, Bryan B., Weed, Natalie, Omstead, Victoria, Bishaw, Yemeserach, Shapovalova, Nadiya V., Martinez, Refugio A., Fong, Olivia, Yao, Shenqin, Mortrud, Marty, Chong, Peter, Loftus, Luke, Bertagnolli, Darren, Goldy, Jeff, Casper, Tamara, Dee, Nick, Opitz-Araya, Ximena, Cetin, Ali, Smith, Kimberly A., Gwinn, Ryder P., Cobbs, Charles, Ko, Andrew L., Ojemann, Jeffrey G., Keene, C. Dirk, Silbergeld, Daniel L., Sunkin, Susan M., Gradinaru, Viviana, Horwitz, Gregory D., Zeng, Hongkui, Tasic, Bosiljka, Lein, Ed S., Ting, Jonathan T., and Levi, Boaz P.

Published
2021
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7. Alternating sources of perisomatic inhibition during behavior

Author

Dudok, Barna, Klein, Peter M., Hwaun, Ernie, Lee, Brian R., Yao, Zizhen, Fong, Olivia, Bowler, John C., Terada, Satoshi, Sparks, Fraser T., Szabo, Gergely G., Farrell, Jordan S., Berg, Jim, Daigle, Tanya L., Tasic, Bosiljka, Dimidschstein, Jordane, Fishell, Gord, Losonczy, Attila, Zeng, Hongkui, and Soltesz, Ivan

Published
2021
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8. Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

Author

Whitesell, Jennifer D., Liska, Adam, Coletta, Ludovico, Hirokawa, Karla E., Bohn, Phillip, Williford, Ali, Groblewski, Peter A., Graddis, Nile, Kuan, Leonard, Knox, Joseph E., Ho, Anh, Wakeman, Wayne, Nicovich, Philip R., Nguyen, Thuc Nghi, van Velthoven, Cindy T.J., Garren, Emma, Fong, Olivia, Naeemi, Maitham, Henry, Alex M., Dee, Nick, Smith, Kimberly A., Levi, Boaz, Feng, David, Ng, Lydia, Tasic, Bosiljka, Zeng, Hongkui, Mihalas, Stefan, Gozzi, Alessandro, and Harris, Julie A.

Published
2021
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9. Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells

Author

Gouwens, Nathan W., Sorensen, Staci A., Baftizadeh, Fahimeh, Budzillo, Agata, Lee, Brian R., Jarsky, Tim, Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Crichton, Kirsten, Daigle, Tanya L., Dalley, Rachel, de Frates, Rebecca A., Dee, Nick, Desta, Tsega, Lee, Samuel Dingman, Dotson, Nadezhda, Egdorf, Tom, Ellingwood, Lauren, Enstrom, Rachel, Esposito, Luke, Farrell, Colin, Feng, David, Fong, Olivia, Gala, Rohan, Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hawrylycz, Michael J., Henry, Alex M., Hill, DiJon, Hupp, Madie, Kebede, Sara, Kim, Tae Kyung, Kim, Lisa, Kroll, Matthew, Lee, Changkyu, Link, Katherine E., Mallory, Matthew, Mann, Rusty, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Mukora, Alice, Ng, Lindsay, Ng, Lydia, Ngo, Kiet, Nicovich, Philip R., Oldre, Aaron, Park, Daniel, Peng, Hanchuan, Penn, Osnat, Pham, Thanh, Pom, Alice, Popović, Zoran, Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Robertson, Miranda, Ronellenfitch, Kara, Ruiz, Augustin, Sandman, David, Smith, Kimberly, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Ward, Katelyn, Williams, Grace, Zhou, Zhi, Ting, Jonathan T., Arkhipov, Anton, Sümbül, Uygar, Lein, Ed S., Koch, Christof, Yao, Zizhen, Tasic, Bosiljka, Berg, Jim, Murphy, Gabe J., and Zeng, Hongkui

Published
2020
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12. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

Author

Daigle, Tanya L., Madisen, Linda, Hage, Travis A., Valley, Matthew T., Knoblich, Ulf, Larsen, Rylan S., Takeno, Marc M., Huang, Lawrence, Gu, Hong, Larsen, Rachael, Mills, Maya, Bosma-Moody, Alice, Siverts, La’ Akea, Walker, Miranda, Graybuck, Lucas T., Yao, Zizhen, Fong, Olivia, Nguyen, Thuc Nghi, Garren, Emma, Lenz, Garreck H., Chavarha, Mariya, Pendergraft, Julie, Harrington, James, Hirokawa, Karla E., Harris, Julie A., Nicovich, Philip R., McGraw, Medea J., Ollerenshaw, Douglas R., Smith, Kimberly A., Baker, Christopher A., Ting, Jonathan T., Sunkin, Susan M., Lecoq, Jérôme, Lin, Michael Z., Boyden, Edward S., Murphy, Gabe J., da Costa, Nuno M., Waters, Jack, Li, Lu, Tasic, Bosiljka, and Zeng, Hongkui

Published
2018
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13. 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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14. 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, Goldy, Jeff, Garren, Emma, Economo, Michael N., Viswanathan, Sarada, Penn, Osnat, Bakken, Trygve, Menon, Vilas, Miller, Jeremy, Fong, Olivia, Hirokawa, Karla E., Lathia, Kanan, Rimorin, Christine, Tieu, Michael, Larsen, Rachael, Casper, Tamara, Barkan, Eliza, Kroll, Matthew, Parry, Sheana, Shapovalova, Nadiya V., Hirschstein, Daniel, Pendergraft, Julie, Sullivan, Heather A., Kim, Tae Kyung, Szafer, Aaron, Dee, Nick, Groblewski, Peter, Wickersham, Ian, Cetin, Ali, Harris, Julie A., Levi, Boaz P., Sunkin, Susan M., Madisen, Linda, Daigle, Tanya L., Looger, Loren, Bernard, Amy, Phillips, John, Lein, Ed, Hawrylycz, Michael, Svoboda, Karel, Jones, Allan R., Koch, Christof, and Zeng, Hongkui

Published
2018
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16. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

Author

McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Media Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Daigle, Tanya L., Madisen, Linda, Hage, Travis A., Valley, Matthew T., Knoblich, Ulf, Larsen, Rylan S., Takeno, Marc M., Huang, Lawrence, Gu, Hong, Larsen, Rachael, Mills, Maya, Bosma-Moody, Alice, Siverts, La’ Akea, Walker, Miranda, Graybuck, Lucas T., Yao, Zizhen, Fong, Olivia, Nguyen, Thuc Nghi, Garren, Emma, Lenz, Garreck H., Chavarha, Mariya, Pendergraft, Julie, Harrington, James, Hirokawa, Karla E., Harris, Julie A., Nicovich, Philip R., McGraw, Medea J., Ollerenshaw, Douglas R., Smith, Kimberly A., Baker, Christopher A., Ting, Jonathan T., Sunkin, Susan M., Lecoq, Jérôme, Lin, Michael Z., Boyden, Edward S., Murphy, Gabe J., da Costa, Nuno M., Waters, Jack, Li, Lu, Tasic, Bosiljka, Zeng, Hongkui, McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Media Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Daigle, Tanya L., Madisen, Linda, Hage, Travis A., Valley, Matthew T., Knoblich, Ulf, Larsen, Rylan S., Takeno, Marc M., Huang, Lawrence, Gu, Hong, Larsen, Rachael, Mills, Maya, Bosma-Moody, Alice, Siverts, La’ Akea, Walker, Miranda, Graybuck, Lucas T., Yao, Zizhen, Fong, Olivia, Nguyen, Thuc Nghi, Garren, Emma, Lenz, Garreck H., Chavarha, Mariya, Pendergraft, Julie, Harrington, James, Hirokawa, Karla E., Harris, Julie A., Nicovich, Philip R., McGraw, Medea J., Ollerenshaw, Douglas R., Smith, Kimberly A., Baker, Christopher A., Ting, Jonathan T., Sunkin, Susan M., Lecoq, Jérôme, Lin, Michael Z., Boyden, Edward S., Murphy, Gabe J., da Costa, Nuno M., Waters, Jack, Li, Lu, Tasic, Bosiljka, and Zeng, Hongkui

Abstract

An expanded toolkit of transgenic mouse lines for exploring the organization, function, and development of mammalian neural circuits.

Published
2022

17. 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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19. 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

21. Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence

Author

Talla, Aarthi, primary, Vasaikar, Suhas V., additional, Lemos, Maria P., additional, Moodie, Zoe, additional, Lee Pebworth, Mark-Phillip, additional, Henderson, Kathy E., additional, Cohen, Kristen W., additional, Czartoski, Julie L., additional, Lai, Lilin, additional, Suthar, Mehul S., additional, Heubeck, Alexander T, additional, Genge, Palak C., additional, Roll, Charles R., additional, Weiss, Morgan, additional, Reading, Julian, additional, Kondza, Nina, additional, MacMillan, Hugh, additional, Fong, Olivia C., additional, Thomson, Zachary James, additional, Graybuck, Lucas T., additional, Okada, Lauren Y., additional, Newell, Evan W., additional, Coffey, Ernest M., additional, Meijer, Paul, additional, Becker, Lynne A., additional, De Rosa, Stephen C., additional, Skene, Peter J., additional, Torgerson, Troy R., additional, Li, Xiao-jun, additional, Szeto, Gregory Lee, additional, McElrath, M. Juliana, additional, and Bumol, Thomas F., additional

Published
2021
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22. Regional, layer, and cell-class specific connectivity of the mouse default mode network

Author

Whitesell, Jennifer D., primary, Liska, Adam, additional, Coletta, Ludovico, additional, Hirokawa, Karla E., additional, Bohn, Phillip, additional, Williford, Ali, additional, Groblewski, Peter A., additional, Graddis, Nile, additional, Kuan, Leonard, additional, Knox, Joseph E., additional, Ho, Anh, additional, Wakeman, Wayne, additional, Nicovich, Philip R., additional, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, van Velthoven, Cindy T. J., additional, Fong, Olivia, additional, Feng, David, additional, Naeemi, Maitham, additional, Henry, Alex M., additional, Dee, Nick, additional, Smith, Kimberly A., additional, Levi, Boaz P., additional, Ng, Lydia, additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, Mihalas, Stefan, additional, Gozzi, Alessandro, additional, and Harris, Julie A., additional

Published
2020
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23. Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Author

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

Published
2020
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24. 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

25. Epigenetic landscape and AAV targeting of human neocortical cell classes

Author

Mich, John K., Hess, Erik E., Graybuck, Lucas T., Somasundaram, Saroja, Miller, Jeremy A., Ding, Yi, Shapovalova, Nadiya V., Fong, Olivia, Yao, Shenqin, Mortrud, Marty, Chong, Peter, Bertagnolli, Darren, Goldy, Jeff, Casper, Tamara, Kroll, Matthew, Hodge, Rebecca D., Bakken, Trygve E., Yao, Zizhen, Dee, Nick, Cetin, Ali, Smith, Kimberly A., Gwinn, Ryder P., Cobbs, Charles, Ko, Andrew. L., Ojemann, Jeffrey G., Keene, C. Dirk, Silbergeld, Daniel. L., Gradinaru, Viviana, Sunkin, Susan M., Zeng, Hongkui, Lein, Ed S., Tasic, Bosiljka, Ting, Jonathan T., and Levi, Boaz P.

Abstract

Myriad cell types comprise the human neocortex, but their roles in normal brain function and disease are largely unknown because few tools exist. To find enhancer elements useful for cell type-specific genetic tools, we examined chromatin accessibility in >2,800 high-quality single human neocortical nuclei. Accessible elements frequently are conserved in mouse (34%), often overlap with hypomethylated sites (27%), and connect cell types with neurological diseases via trait-associated SNPs. Directly testing these elements in viral vectors demonstrates functional enhancer activity with cell type specificity predicted by their chromatin accessibility patterns. In summary we present a catalog of human cell class-specific epigenetic elements, and utilize them for new species-agnostic cell type-specific viral genetic tools, which will illuminate human neuron function and drive gene therapy applications. One sentence summary Mapping chromatin accessibility in human brain cell classes links gene regulation to disease and enables human genetic tools.

Published
2019
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26. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Author

Yao, Zizhen, primary, Nguyen, Thuc Nghi, additional, van Velthoven, Cindy T. J., additional, Goldy, Jeff, additional, Sedeno-Cortes, Adriana E., additional, Baftizadeh, Fahimeh, additional, Bertagnolli, Darren, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Ding, Song-Lin, additional, Fong, Olivia, additional, Garren, Emma, additional, Glandon, Alexandra, additional, Gray, James, additional, Graybuck, Lucas T., additional, Hirschstein, Daniel, additional, Kroll, Matthew, additional, Lathia, Kanan, 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
2020
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27. An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Author

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

Published
2020
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28. Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

Author

Gouwens, Nathan W., primary, Sorensen, Staci A., additional, Baftizadeh, Fahimeh, additional, Budzillo, Agata, additional, Lee, Brian R., additional, Jarsky, Tim, additional, Alfiler, Lauren, additional, Arkhipov, Anton, additional, Baker, Katherine, additional, Barkan, Eliza, additional, Berry, Kyla, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bomben, Jasmine, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Daigle, Tanya L., additional, Dalley, Rachel, additional, de Frates, Rebecca, additional, Dee, Nick, additional, Desta, Tsega, additional, Lee, Samuel Dingman, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Ellingwood, Lauren, additional, Enstrom, Rachel, additional, Esposito, Luke, additional, Farrell, Colin, additional, Feng, David, additional, Fong, Olivia, additional, Gala, Rohan, additional, Gamlin, Clare, additional, Gary, Amanda, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Gorham, Melissa, additional, Graybuck, Lucas, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hawrylycz, Michael J., additional, Henry, Alex M., additional, Hill, DiJon, additional, Hupp, Madie, additional, Kebede, Sara, additional, Kim, Tae Kyung, additional, Kim, Lisa, additional, Kroll, Matthew, additional, Lee, Changkyu, additional, Link, Katherine E., additional, Mallory, Matthew, additional, Mann, Rusty, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Oldre, Aaron, additional, Park, Daniel, additional, Peng, Hanchuan, additional, Penn, Osnat, additional, Pham, Thanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Ransford, Shea, additional, Reid, David, additional, Rimorin, Christine, additional, Robertson, Miranda, additional, Ronellenfitch, Kara, additional, Ruiz, Augustin, additional, Sandman, David, additional, Smith, Kimberly, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Szafer, Aaron, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Trinh, Jessica, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Ward, Katelyn, additional, Williams, Grace, additional, Zhou, Zhi, additional, Ting, Jonathan, additional, Sumbul, Uygar, additional, Lein, Ed, additional, Koch, Christof, additional, Yao, Zizhen, additional, Tasic, Bosiljka, additional, Berg, Jim, additional, Murphy, Gabe J., additional, and Zeng, Hongkui, additional

Published
2020
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29. Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex

Author

Mich, John K., primary, Graybuck, Lucas T., additional, Hess, Erik, additional, Mahoney, Joseph, additional, Kojima, Yoshiko, additional, Ding, Yi, additional, Somasundaram, Saroja, additional, Miller, Jeremy A., additional, Weed, Natalie, additional, Omstead, Victoria, additional, Bishaw, Yemeserach, additional, Shapovalova, Nadiya, additional, Martinez, Refugio, 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, additional, Ting, Jonathan, additional, and Levi, Boaz, additional

Published
2020
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30. Toward an Integrated Classification of Cell Types: Morphoelectric and Transcriptomic Characterization of Individual GABAergic Cortical Neurons

Author

Gouwens, Nathan W., primary, Sorensen, Staci A., additional, Baftizadeh, Fahimeh, additional, Budzillo, Agata, additional, Lee, Brian R., additional, Jarsky, Tim, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Barkan, Eliza, additional, Berry, Kyla, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bomben, Jasmine, additional, Braun, Thomas, additional, Brouner, Kirssy, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Daigle, Tanya L., additional, Dalley, Rachel, additional, de Frates, Rebeeca, additional, Dee, Nick, additional, Desta, Tsega, additional, Dingman Lee, Samuel, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Ellingwood, Lauren, additional, Enstrom, Rachel, additional, Esposito, Luke, additional, Farrell, Colin, additional, Feng, David, additional, Fong, Olivia, additional, Gala, Rohan, additional, Gamlin, Clare, additional, Gary, Amanda, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Gorham, Melissa, additional, Graybuck, Lucas, additional, Gu, Hong, additional, Hadley, Kirsten, additional, Hawrylycz, Michael J., additional, Henry, Alex M., additional, Hill, DiJon, additional, Happ, Madie, additional, Kebede, Sara, additional, Kyung Kim, Tae, additional, Kim, Lisa, additional, Kroll, Matthew, additional, Lee, Changkyu, additional, Link, Katherine E., additional, Mallory, Matthew, additional, Mann, Rusty, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Oldre, Aaron, additional, Park, Daniel, additional, Peng, Hanchuan, additional, Penn, Osnat, additional, Pham, Thanh, additional, Pom, Alice, additional, Potekhina, Lyida, additional, Rajanbabu, Ramkumar, additional, Ransford, Shea, additional, Reid, David, additional, Rimorin, Christine, additional, Robertson, Miranda, additional, Ronellenfitch, Kara, additional, Ruiz, Augustin, additional, Sandman, David, additional, Smith, Kimberly, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Szafer, Aaron, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Trinh, Jessica, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Ward, Katelyn, additional, Williams, Grace, additional, Zhou, Zhi, additional, Ting, Jonathan, additional, Arkhipov, Anton, additional, Sumbul, Uygar, additional, Lein, Ed, additional, Koch, Christof, additional, Yao, Zizhen, additional, Tasic, Bosiljka, additional, Berg, Jim, additional, Murphy, Gabe J., additional, and Zeng, Hongkui, additional

Published
2020
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31. Distinct transcriptomic cell types and neural circuits of the subiculum and prosubiculum along the dorsal-ventral axis

Author

Ding, Song-Lin, primary, Yao, Zizhen, additional, Hirokawa, Karla E., additional, Nguyen, Thuc Nghi, additional, Graybuck, Lucas T., additional, Fong, Olivia, additional, Bohn, Phillip, additional, Ngo, Kiet, additional, Smith, Kimberly A., additional, Koch, Christof, additional, Phillips, John W., additional, Lein, Ed S., additional, Harris, Julie A., additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional

Published
2019
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32. 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, 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
2019
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33. Conserved cell types with divergent features between human and mouse cortex

Author

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

Published
2018
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34. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain Cell Type Targeting and Functionality

Author

Daigle, Tanya L., primary, Madisen, Linda, additional, Hage, Travis A., additional, Valley, Matthew T., additional, Knoblich, Ulf, additional, Larsen, Rylan S., additional, Takeno, Marc M., additional, Huang, Lawrence, additional, Gu, Hong, additional, Larsen, Rachael, additional, Mills, Maya, additional, Bosma-Moody, Alice, additional, Siverts, La'Akea, additional, Walker, Miranda, additional, Graybuck, Lucas T., additional, Yao, Zizhen, additional, Fong, Olivia, additional, Garren, Emma, additional, Lenz, Garreck, additional, Chavarha, Mariya, additional, Pendergraft, Julie, additional, Harrington, James, additional, Hirokawa, Karla E., additional, Harris, Julie A., additional, McGraw, Medea, additional, Ollerenshaw, Douglas R., additional, Smith, Kimberly, additional, Baker, Christopher A., additional, Ting, Jonathan T., additional, Sunkin, Susan M., additional, Lecoq, Jerome, additional, Lin, Michael Z., additional, Boyden, Edward S., additional, Murphy, Gabe J., additional, da Costa, Nuno, additional, Waters, Jack, additional, Li, Lu, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional

Published
2018
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35. Shared and distinct transcriptomic cell types across neocortical areas

Author

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

Published
2017
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36. A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

Author

Daigle, Tanya L., primary, Madisen, Linda, additional, Hage, Travis A., additional, Valley, Matthew T., additional, Knoblich, Ulf, additional, Larsen, Rylan S., additional, Takeno, Marc M., additional, Huang, Lawrence, additional, Gu, Hong, additional, Larsen, Rachael, additional, Mills, Maya, additional, Bosma-Moody, Alice, additional, Siverts, La’Akea, additional, Walker, Miranda, additional, Graybuck, Lucas T., additional, Yao, Zizhen, additional, Fong, Olivia, additional, Garren, Emma, additional, Lenz, Garreck, additional, Chavarha, Mariya, additional, Pendergraft, Julie, additional, Harrington, James, additional, Hirokawa, Karla E., additional, Harris, Julie A., additional, McGraw, Medea, additional, Ollerenshaw, Douglas R., additional, Smith, Kimberly, additional, Baker, Christopher A., additional, Ting, Jonathan T., additional, Sunkin, Susan M., additional, Lecoq, Jerome, additional, Lin, Michael Z., additional, Boyden, Edward S., additional, Murphy, Gabe J., additional, da Costa, Nuno, additional, Waters, Jack, additional, Li, Lu, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional

Published
2017
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38. Form Follows Food: An examination of architecture's role in urban farming

Author

Gjerde, Morten, Fong, Olivia, Gjerde, Morten, and Fong, Olivia

Abstract

With rising global urban populations, existing food infrastructure systems are rapidly becoming unsustainable. Increasing distances between rural food production and urban residents extends to a conceptual divide and misguided understanding of what activities ought to be classed as ‘rural’ versus ‘urban’. Some of those looking for alternative solutions note food’s potential to act as an organiser of urban systems and catalyst for sustainable living. However the concept of sustainability is often sidelined in photorealistic renders where designs are decorated with organic matter, designs that are unlikely to be viable. Tapping into food’s potential and with the readily available space of urban rooftops, the thesis explores rooftop urban farming to speculate the opportunities it presents in the city of Wellington, New Zealand. In relation to this important social, economic and ecological infrastructure, the thesis investigates how the potential for urban farming, from production to trading and consumption contributes to a sense of place through architectural interpretation. While widening the discussions of food and the city, architecture provides the built accommodation for both plants and people, so that the ‘urban future’ can be reevaluated.

Published
2017

39. Form Follows Food : an examination of architecture's role in urban farming : a 120-point thesis submitted to the Victoria University of Wellington in partial fulfilment of the requirements for the degree of Master of Architecture (Professional)

Author

Fong, Olivia and Fong, Olivia

Subjects
Architectural design Environmental aspects New Zealand Wellington., Urban agriculture New Zealand Wellington., Architecture Environmental aspects New Zealand Wellington., Sustainable urban development New Zealand Wellington., Design architectural Aspect de l'environnement Nouvelle-Zélande Wellington., Agriculture urbaine Nouvelle-Zélande Wellington., Architecture Aspect de l'environnement Nouvelle-Zélande Wellington., Urbanisme durable Nouvelle-Zélande Wellington., Architectural design Environmental aspects., Architecture Environmental aspects., Sustainable urban development., Urban agriculture., New Zealand Wellington.
Abstract

With rising global urban populations, existing food infrastructure systems are rapidly becoming unsustainable. Increasing distances between rural food production and urban residents extends to a conceptual divide and misguided understanding of what activities ought to be classed as 'rural' versus 'urban'. Some of those looking for alternative solutions note food's potential to act as an organiser of urban systems and catalyst for sustainable living. However the concept of sustainability is often sidelined in photorealistic renders where designs are decorated with organic matter, designs that are unlikely to be viable. Tapping into food's potential and with the readily available space of urban rooftops, the thesis explores rooftop urban farming to speculate the opportunities it presents in the city of Wellington, New Zealand. In relation to this important social, economic and ecological infrastructure, the thesis investigates how the potential for urban farming, from production to trading and consumption contributes to a sense of place through architectural interpretation. While widening the discussions of food and the city, architecture provides the built accommodation for both plants and people, so that the 'urban future' can be reevaluated.

Published
2017

40. Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence.

Author

Talla A, Vasaikar SV, Lemos MP, Moodie Z, Lee Pebworth MP, Henderson KE, Cohen KW, Czartoski JL, Lai L, Suthar MS, Heubeck AT, Genge PC, Roll CR, Weiss M, Reading J, Kondza N, MacMillan H, Fong OC, Thomson ZJ, Graybuck LT, Okada LY, Newell EW, Coffey EM, Meijer P, Becker LA, De Rosa SC, Skene PJ, Torgerson TR, Li XJ, Szeto GL, McElrath MJ, and Bumol TF

Abstract

SARS-CoV-2 has infected over 200 million and caused more than 4 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID-19 beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive immune activation that differed in character by age (young vs. old). We then characterized signals associated with recovery and convalescence to define and validate a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).

Published
2021
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