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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. 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

3. 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

4. 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

5. Morphological diversity of single neurons in molecularly defined cell types

Author

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

Published
2021
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6. Identification of preoptic sleep neurons using retrograde labelling and gene profiling.

Author

Chung, Shinjae, Weber, Franz, Zhong, Peng, Tan, Chan Lek, Nguyen, Thuc Nghi, Beier, Kevin T, Hörmann, Nikolai, Chang, Wei-Cheng, Zhang, Zhe, Do, Johnny Phong, Yao, Shenqin, Krashes, Michael J, Tasic, Bosiljka, Cetin, Ali, Zeng, Hongkui, Knight, Zachary A, Luo, Liqun, and Dan, Yang

Subjects
Hypothalamic Area, Lateral, Preoptic Area, Neurons, Ribosomes, Animals, Mice, Cholecystokinin, Corticotropin-Releasing Hormone, Tachykinins, Chloride Channels, Proto-Oncogene Proteins c-fos, Sequence Analysis, RNA, Wakefulness, Sleep, Female, Male, Neuroanatomical Tract-Tracing Techniques, Single-Cell Analysis, Transcriptome, GABAergic Neurons, Optogenetics, Biomarkers, Channelrhodopsins, Hypothalamic Area, Lateral, Sequence Analysis, RNA, General Science & Technology
Abstract

In humans and other mammalian species, lesions in the preoptic area of the hypothalamus cause profound sleep impairment, indicating a crucial role of the preoptic area in sleep generation. However, the underlying circuit mechanism remains poorly understood. Electrophysiological recordings and c-Fos immunohistochemistry have shown the existence of sleep-active neurons in the preoptic area, especially in the ventrolateral preoptic area and median preoptic nucleus. Pharmacogenetic activation of c-Fos-labelled sleep-active neurons has been shown to induce sleep. However, the sleep-active neurons are spatially intermingled with wake-active neurons, making it difficult to target the sleep neurons specifically for circuit analysis. Here we identify a population of preoptic area sleep neurons on the basis of their projection target and discover their molecular markers. Using a lentivirus expressing channelrhodopsin-2 or a light-activated chloride channel for retrograde labelling, bidirectional optogenetic manipulation, and optrode recording, we show that the preoptic area GABAergic neurons projecting to the tuberomammillary nucleus are both sleep active and sleep promoting. Furthermore, translating ribosome affinity purification and single-cell RNA sequencing identify candidate markers for these neurons, and optogenetic and pharmacogenetic manipulations demonstrate that several peptide markers (cholecystokinin, corticotropin-releasing hormone, and tachykinin 1) label sleep-promoting neurons. Together, these findings provide easy genetic access to sleep-promoting preoptic area neurons and a valuable entry point for dissecting the sleep control circuit.

Published
2017

9. A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

Author

Thompson, Carol L, Ng, Lydia, Menon, Vilas, Martinez, Salvador, Lee, Chang-Kyu, Glattfelder, Katie, Sunkin, Susan M, Henry, Alex, Lau, Christopher, Dang, Chinh, Garcia-Lopez, Raquel, Martinez-Ferre, Almudena, Pombero, Ana, Rubenstein, John LR, Wakeman, Wayne B, Hohmann, John, Dee, Nick, Sodt, Andrew J, Young, Rob, Smith, Kimberly, Nguyen, Thuc-Nghi, Kidney, Jolene, Kuan, Leonard, Jeromin, Andreas, Kaykas, Ajamete, Miller, Jeremy, Page, Damon, Orta, Geri, Bernard, Amy, Riley, Zackery, Smith, Simon, Wohnoutka, Paul, Hawrylycz, Michael J, Puelles, Luis, and Jones, Allan R

Subjects
Neurosciences, Biotechnology, Genetics, Pediatric, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

Published
2014

10. 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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11. Classification of electrophysiological and morphological neuron types in the mouse visual cortex

Author

Gouwens, Nathan W., Sorensen, Staci A., Berg, Jim, Lee, Changkyu, Jarsky, Tim, Ting, Jonathan, Sunkin, Susan M., Feng, David, Anastassiou, Costas A., Barkan, Eliza, Bickley, Kris, Blesie, Nicole, Braun, Thomas, Brouner, Krissy, Budzillo, Agata, Caldejon, Shiella, Casper, Tamara, Castelli, Dan, Chong, Peter, Crichton, Kirsten, Cuhaciyan, Christine, Daigle, Tanya L., Dalley, Rachel, Dee, Nick, Desta, Tsega, Ding, Song-Lin, Dingman, Samuel, Doperalski, Alyse, Dotson, Nadezhda, Egdorf, Tom, Fisher, Michael, de Frates, Rebecca A., Garren, Emma, Garwood, Marissa, Gary, Amanda, Gaudreault, Nathalie, Godfrey, Keith, Gorham, Melissa, Gu, Hong, Habel, Caroline, Hadley, Kristen, Harrington, James, Harris, Julie A., Henry, Alex, Hill, DiJon, Josephsen, Sam, Kebede, Sara, Kim, Lisa, Kroll, Matthew, Lee, Brian, Lemon, Tracy, Link, Katherine E., Liu, Xiaoxiao, Long, Brian, Mann, Rusty, McGraw, Medea, Mihalas, Stefan, Mukora, Alice, Murphy, Gabe J., Ng, Lindsay, Ngo, Kiet, Nguyen, Thuc Nghi, Nicovich, Philip R., Oldre, Aaron, Park, Daniel, Parry, Sheana, Perkins, Jed, Potekhina, Lydia, Reid, David, Robertson, Miranda, Sandman, David, Schroedter, Martin, Slaughterbeck, Cliff, Soler-Llavina, Gilberto, Sulc, Josef, Szafer, Aaron, Tasic, Bosiljka, Taskin, Naz, Teeter, Corinne, Thatra, Nivretta, Tung, Herman, Wakeman, Wayne, Williams, Grace, Young, Rob, Zhou, Zhi, Farrell, Colin, Peng, Hanchuan, Hawrylycz, Michael J., Lein, Ed, Ng, Lydia, Arkhipov, Anton, Bernard, Amy, Phillips, John W., Zeng, Hongkui, and Koch, Christof

Published
2019
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14. 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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15. 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, Zeng, Hongkui, 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. 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

18. A mesoscale connectome of the mouse brain

Author

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

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

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

Published
2014
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19. 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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20. 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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21. 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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22. 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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24. Regional, Layer, and Cell-Type-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, van Velthoven, Cindy T.J., additional, Garren, Emma, additional, Fong, Olivia, additional, Naeemi, Maitham, additional, Henry, Alex M., additional, Dee, Nick, additional, Smith, Kimberly A., additional, Levi, Boaz, additional, Feng, David, additional, Ng, Lydia, additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, Mihalas, Stefan, additional, Gozzi, Alessandro, additional, and Harris, Julie A., additional

Published
2021
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25. 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

26. 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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27. 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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28. 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
2020
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29. 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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30. 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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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. Complete single neuron reconstruction reveals morphological diversity in molecularly defined claustral and cortical neuron types

Author

Wang, Yun, Xie, Peng, Gong, Hui, Zhou, Zhi, Kuang, Xiuli, Wang, Yimin, Li, An-an, Li, Yaoyao, Liu, Lijuan, Veldman, Matthew B., Daigle, Tanya L., Hirokawa, Karla E., Qu, Lei, Lesnar, Phil, Jiang, Shengdian, Yu, Yang, Wakeman, Wayne, Zeng, Shaoqun, Li, Xiangning, Yuan, Jing, Nguyen, Thuc Nghi, Larsen, Rachael, Kebede, Sara, Song, Yuanyuan, Yin, Lulu, Zhao, Sujun, Feiner, Aaron, Shen, Elise, Hill, Chris, Wang, Quanxin, Mok, Stephanie, Sunkin, Susan M., Josh Huang, Z., Esposito, Luke, Yao, Zizhen, Hawrylycz, Michael J., Tasic, Bosiljka, Ng, Lydia, Sorensen, Staci A., William Yang, X., Harris, Julie A., Koch, Christof, Luo, Qingming, Peng, Hanchuan, and Zeng, Hongkui

Abstract

SUMMARY Ever since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types and their connectivity. Yet our knowledge about the diversity of neuronal morphology, in particular its distant axonal projections, is still extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale in mice, we established a pipeline that encompasses five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types across the mouse brain in an efficient way by combining transgenic or viral Cre delivery with novel transgenic reporter lines, and generated a large set of high-resolution whole-brain fluorescent imaging datasets containing thousands of reconstructable neurons using the fluorescence micro-optical sectioning tomography (fMOST) system. We developed a set of software tools based on the visualization and analysis suite, Vaa3D, for large-volume image data processing and computation-assisted morphological reconstruction. In a proof-of-principle case, we reconstructed full morphologies of 96 neurons from the claustrum and cortex that belong to a single transcriptomically-defined neuronal subclass. We developed a data-driven clustering approach to classify them into multiple morphological and projection types, suggesting that these neurons work in a targeted and coordinated manner to process cortical information. Imaging data and the new computational reconstruction tools are publicly available to enable community-based efforts towards large-scale full morphology reconstruction of neurons throughout the entire mouse brain.

Published
2019
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33. Prospective, brain-wide labeling of neuronal subclasses with enhancer-driven AAVs

Author

Graybuck, Lucas T., Sedeño-Cortés, Adriana E., Nguyen, Thuc Nghi, Walker, Miranda, Szelenyi, Eric, Lenz, Garreck, Sieverts, La’Akea, Kim, Tae Kyung, Garren, Emma, Kalmbach, Brian, Yao, Shenqin, Mortrud, Marty, Mich, John, Goldy, Jeff, Smith, Kimberly, Dee, Nick, Yao, Zizhen, Cetin, Ali, Levi, Boaz, Lein, Ed, Ting, Jonathan, Zeng, Hongkui, Daigle, Tanya, and Tasic, Bosiljka

Abstract

Labeling and perturbation of specific cell types in multicellular systems has transformed our ability to understand them. The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient access to these newly discovered types. To enable access to specific neural populations in the mouse cortex, we have collected single cell chromatin accessibility data from select cell types. We clustered the single cell data and mapped them to single cell transcriptomics to identify highly specific enhancers for cell subclasses. These enhancers, when cloned into AAVs and delivered to the brain by retro orbital injections, transgene expression in specific cell subclasses throughout the mouse brain. This approach will enable functional investigation of cell types in the mouse cortex and beyond. One sentence Summary Combining scATAC-seq and scRNA-seq identifies subclass-specific enhancers to label cells in mouse cortex at high resolution

Published
2019
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34. Cell segmentation-free inference of cell types from in situ transcriptomics data

Author

Park, Jeongbin, primary, Choi, Wonyl, additional, Tiesmeyer, Sebastian, additional, Long, Brian, additional, Borm, Lars E., additional, Garren, Emma, additional, Nguyen, Thuc Nghi, additional, Tasic, Bosiljka, additional, Codeluppi, Simone, additional, Graf, Tobias, additional, Schlesner, Matthias, additional, Stegle, Oliver, additional, Eils, Roland, additional, and Ishaque, Naveed, additional

Published
2019
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35. Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

Author

Kim, Dong-Wook, primary, Yao, Zizhen, additional, Graybuck, Lucas T., additional, Kim, Tae Kyung, additional, Nguyen, Thuc Nghi, additional, Smith, Kimberly A., additional, Fong, Olivia, additional, Yi, Lynn, additional, Koulena, Noushin, additional, Pierson, Nico, additional, Shah, Sheel, additional, Lo, Liching, additional, Pool, Allan-Hermann, additional, Oka, Yuki, additional, Pachter, Lior, additional, Cai, Long, additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, and Anderson, David J., additional

Published
2019
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37. Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types

Author

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

Published
2019
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38. Enhancer viruses and a transgenic platform 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, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, Kim, Tae Kyung, additional, Siverts, La’ Akea, additional, Bendrick, Jacqueline L., additional, Zhou, Thomas, additional, Mortrud, Marty, additional, Yao, Shenqin, additional, Cetin, Ali H., additional, Larsen, Rachael, additional, Esposito, Luke, additional, Gore, Bryan, additional, Szelenyi, Eric, additional, Morin, Elyse, additional, Mich, John K., additional, Dee, Nick, additional, Goldy, Jeff, additional, Smith, Kimberly, 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
2019
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39. Multimodal cell type correspondence by intersectional mFISH in intact tissues

Author

Nicovich, Philip R., primary, Taormina, Michael J., additional, Baker, Christopher A., additional, Nguyen, Thuc Nghi, additional, Thomsen, Elliot R., additional, Garren, Emma, additional, Long, Brian, additional, Gorham, Melissa, additional, Miller, Jeremy A., additional, Hage, Travis, additional, Bosma-Moody, Alice, additional, Murphy, Gabe J., additional, Levi, Boaz P., additional, Close, Jennie L., additional, Tasic, Bosiljka, additional, Lein, Ed S., additional, and Zeng, Hongkui, additional

Published
2019
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40. Complete Whole-Brain Single Neuron Reconstruction Reveals Morphological Diversity in Molecularly Defined Claustral and Cortical Neuron Types

Author

Wang, Yun, primary, Xie, Peng, additional, Gong, Hui, additional, Zhou, Zhi, additional, Kuang, Xiuli, additional, Wang, Yimin, additional, Li, Anan, additional, Li, Yaoyao, additional, Liu, Lijuan, additional, Veldman, Matthew B., additional, Daigle, Tanya L., additional, Hirokawa, Karla E., additional, Qu, Lei, additional, Lesnar, Philip, additional, Jiang, Shengdian, additional, Yu, Yang, additional, Wakeman, Wayne, additional, Zeng, Shaoqun, additional, Li, Xiangning, additional, Yuan, Jing, additional, Nguyen, Thuc Nghi, additional, Larsen, Rachael, additional, Kebede, Sara, additional, Song, Yuanyuan, additional, Ying, Lulu, additional, Zhao, Sujun, additional, Feiner, Aaron, additional, Shen, Elise, additional, Hill, Chris, additional, Wang, Quanxin, additional, Mok, Stephanie, additional, Sunkin, Susan M., additional, Huang, Z. Josh, additional, Esposito, Luke, additional, Yao, Zizhen, additional, Hawrylycz, Michael J., additional, Tasic, Bosiljka, additional, Ng, Lydia, additional, Sorensen, Staci A., additional, Yang, X. William, additional, Harris, Julie A., additional, Koch, Christof, additional, Luo, Qingming, additional, Peng, Hanchuan, additional, and Zeng, Hongkui, additional

Published
2019
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41. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

Author

Bakken, Trygve E., primary, Hodge, Rebecca D., additional, Miller, Jeremy A., additional, Yao, Zizhen, additional, Nguyen, Thuc Nghi, additional, Aevermann, Brian, additional, Barkan, Eliza, additional, Bertagnolli, Darren, additional, Casper, Tamara, additional, Dee, Nick, additional, Garren, Emma, additional, Goldy, Jeff, additional, Graybuck, Lucas T., additional, Kroll, Matthew, additional, Lasken, Roger S., additional, Lathia, Kanan, additional, Parry, Sheana, additional, Rimorin, Christine, additional, Scheuermann, Richard H., additional, Schork, Nicholas J., additional, Shehata, Soraya I., additional, Tieu, Michael, additional, Phillips, John W., additional, Bernard, Amy, additional, Smith, Kimberly A., additional, Zeng, Hongkui, additional, Lein, Ed S., additional, and Tasic, Bosiljka, additional

Published
2018
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42. Enteroendocrine cells switch hormone expression along the crypt-to-villus BMP signalling gradient

Author

Hubrecht Institute with UMC, CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Cancer, Beumer, Joep, Artegiani, Benedetta, Post, Yorick, Reimann, Frank, Gribble, Fiona, Nguyen, Thuc Nghi, Zeng, Hongkui, Van den Born, Maaike, Van Es, Johan H., Clevers, Hans, Hubrecht Institute with UMC, CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Cancer, Beumer, Joep, Artegiani, Benedetta, Post, Yorick, Reimann, Frank, Gribble, Fiona, Nguyen, Thuc Nghi, Zeng, Hongkui, Van den Born, Maaike, Van Es, Johan H., and Clevers, Hans

Published
2018

43. 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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44. Classification of electrophysiological and morphological types in mouse visual cortex

Author

Gouwens, Nathan W., primary, Sorensen, Staci A., additional, Berg, Jim, additional, Lee, Changkyu, additional, Jarsky, Tim, additional, Ting, Jonathan, additional, Sunkin, Susan M., additional, Feng, David, additional, Anastassiou, Costas, additional, Barkan, Eliza, additional, Bickley, Kris, additional, Blesie, Nicole, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Budzillo, Agata, additional, Caldejon, Shiella, additional, Casper, Tamara, additional, Casteli, Dan, additional, Chong, Peter, additional, Crichton, Kirsten, additional, Cuhaciyan, Christine, additional, Tanya, L. Daigle, additional, Dalley, Rachel, additional, Dee, Nick, additional, Desta, Tsega, additional, Dingman, Samuel, additional, Doperalski, Alyse, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Fisher, Michael, additional, de Frates, Rebecca A., additional, Garren, Emma, additional, Garwood, Marissa, additional, Gary, Amanda, additional, Gaudreault, Nathalie, additional, Godfrey, Keith, additional, Gorham, Melissa, additional, Gu, Hong, additional, Habel, Caroline, additional, Hadley, Kristen, additional, Harrington, James, additional, Harris, Julie, additional, Henry, Alex, additional, Hill, DiJon, additional, Josephsen, Sam, additional, Kebede, Sara, additional, Kim, Lisa, additional, Kroll, Matthew, additional, Lee, Brian, additional, Lemon, Tracy, additional, Liu, Xiaoxiao, additional, Long, Brian, additional, Mann, Rusty, additional, McGraw, Medea, additional, Mihalas, Stefan, additional, Mukora, Alice, additional, Murphy, Gabe J., additional, Ng, Lindsay, additional, Ngo, Kiet, additional, Nguyen, Thuc Nghi, additional, Nicovich, Philip R., additional, Oldre, Aaron, additional, Park, Daniel, additional, Parry, Sheana, additional, Perkins, Jed, additional, Potekhina, Lydia, additional, Reid, David, additional, Robertson, Miranda, additional, Sandman, David, additional, Schroedter, Martin, additional, Slaughterbeck, Cliff, additional, Soler-Llavina, Gilberto, additional, Sulc, Josef, additional, Szafer, Aaron, additional, Tasic, Bosiljka, additional, Taskin, Naz, additional, Teeter, Corinne, additional, Thatra, Nivretta, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Williams, Grace, additional, Young, Rob, additional, Zhou, Zhi, additional, Farrell, Colin, additional, Peng, Hanchuan, additional, Hawrylycz, Michael J., additional, Lein, Ed, additional, Ng, Lydia, additional, Arkhipov, Anton, additional, Bernard, Amy, additional, Phillips, John W., additional, Zeng, Hongkui, additional, and Koch, Christof, additional

Published
2018
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45. 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, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, Lenz, Garreck H., additional, Chavarha, Mariya, additional, Pendergraft, Julie, additional, Harrington, James, additional, Hirokawa, Karla E., additional, Harris, Julie A., additional, Nicovich, Philip R., additional, McGraw, Medea J., additional, Ollerenshaw, Douglas R., additional, Smith, Kimberly A., additional, Baker, Christopher A., additional, Ting, Jonathan T., additional, Sunkin, Susan M., additional, Lecoq, Jérôme, additional, Lin, Michael Z., additional, Boyden, Edward S., additional, Murphy, Gabe J., additional, da Costa, Nuno M., additional, Waters, Jack, additional, Li, Lu, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional

Published
2018
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46. 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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47. Distinct descending motor cortex pathways and their roles in movement

Author

Economo, Michael N., primary, Viswanathan, Sarada, additional, Tasic, Bosiljka, additional, Bas, Erhan, additional, Winnubst, Johan, additional, Menon, Vilas, additional, Graybuck, Lucas T., additional, Nguyen, Thuc Nghi, additional, Wang, Lihua, additional, Gerfen, Charles R., additional, Chandrashekar, Jayaram, additional, Zeng, Hongkui, additional, Looger, Loren L., additional, and Svoboda, Karel, additional

Published
2017
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50. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Author

Tasic, Bosiljka, primary, Menon, Vilas, additional, Nguyen, Thuc Nghi, additional, Kim, Tae Kyung, additional, Jarsky, Tim, additional, Yao, Zizhen, additional, Levi, Boaz, additional, Gray, Lucas T, additional, Sorensen, Staci A, additional, Dolbeare, Tim, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Shapovalova, Nadiya, additional, Parry, Sheana, additional, Lee, Changkyu, additional, Smith, Kimberly, additional, Bernard, Amy, additional, Madisen, Linda, additional, Sunkin, Susan M, additional, Hawrylycz, Michael, additional, Koch, Christof, additional, and Zeng, Hongkui, additional

Published
2016
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