Shared and distinct transcriptomic cell types across neocortical areas

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

doi:10.1038/s41586-018-0654-5

Shared and distinct transcriptomic cell types across neocortical areas

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

Research output: Contribution to journal › Article › peer-review

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 (γ-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.

Original language	English (US)
Pages (from-to)	72-78
Number of pages	7
Journal	Nature
Volume	563
Issue number	7729
DOIs	https://doi.org/10.1038/s41586-018-0654-5
State	Published - Nov 1 2018
Externally published	Yes

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Tasic, B., Yao, Z., Graybuck, L. T., Smith, K. A., Nguyen, T. N., Bertagnolli, D., Goldy, J., Garren, E., Economo, M. N., Viswanathan, S., Penn, O., Bakken, T., Menon, V., Miller, J., Fong, O., Hirokawa, K. E., Lathia, K., Rimorin, C., Tieu, M., ... Zeng, H. (2018). Shared and distinct transcriptomic cell types across neocortical areas. Nature, 563(7729), 72-78. https://doi.org/10.1038/s41586-018-0654-5

Tasic, B, Yao, Z, Graybuck, LT, Smith, KA, Nguyen, TN, Bertagnolli, D, Goldy, J, Garren, E, Economo, MN, Viswanathan, S, Penn, O, Bakken, T, Menon, V, Miller, J, Fong, O, Hirokawa, KE, Lathia, K, Rimorin, C, Tieu, M, Larsen, R, Casper, T, Barkan, E, Kroll, M, Parry, S, Shapovalova, NV, Hirschstein, D, Pendergraft, J, Sullivan, HA, Kim, TK, Szafer, A, Dee, N, Groblewski, P, Wickersham, I, Cetin, A, Harris, JA, Levi, BP, Sunkin, SM, Madisen, L, Daigle, TL, Looger, L, Bernard, A, Phillips, J, Lein, E, Hawrylycz, M, Svoboda, K, Jones, AR, Koch, C & Zeng, H 2018, 'Shared and distinct transcriptomic cell types across neocortical areas', Nature, vol. 563, no. 7729, pp. 72-78. https://doi.org/10.1038/s41586-018-0654-5

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title = "Shared and distinct transcriptomic cell types across neocortical areas",

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 (γ-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.",

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

note = "Publisher Copyright: {\textcopyright} 2018, Springer Nature Limited.",

year = "2018",

month = nov,

day = "1",

doi = "10.1038/s41586-018-0654-5",

language = "English (US)",

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T1 - Shared and distinct transcriptomic cell types across neocortical areas

AU - Tasic, Bosiljka

AU - Yao, Zizhen

AU - Graybuck, Lucas T.

AU - Smith, Kimberly A.

AU - Nguyen, Thuc Nghi

AU - Bertagnolli, Darren

AU - Goldy, Jeff

AU - Garren, Emma

AU - Economo, Michael N.

AU - Viswanathan, Sarada

AU - Penn, Osnat

AU - Bakken, Trygve

AU - Menon, Vilas

AU - Miller, Jeremy

AU - Fong, Olivia

AU - Hirokawa, Karla E.

AU - Lathia, Kanan

AU - Rimorin, Christine

AU - Tieu, Michael

AU - Larsen, Rachael

AU - Casper, Tamara

AU - Barkan, Eliza

AU - Kroll, Matthew

AU - Parry, Sheana

AU - Shapovalova, Nadiya V.

AU - Hirschstein, Daniel

AU - Pendergraft, Julie

AU - Sullivan, Heather A.

AU - Kim, Tae Kyung

AU - Szafer, Aaron

AU - Dee, Nick

AU - Groblewski, Peter

AU - Wickersham, Ian

AU - Cetin, Ali

AU - Harris, Julie A.

AU - Levi, Boaz P.

AU - Sunkin, Susan M.

AU - Madisen, Linda

AU - Daigle, Tanya L.

AU - Looger, Loren

AU - Bernard, Amy

AU - Phillips, John

AU - Lein, Ed

AU - Hawrylycz, Michael

AU - Svoboda, Karel

AU - Jones, Allan R.

AU - Koch, Christof

AU - Zeng, Hongkui

PY - 2018/11/1

Y1 - 2018/11/1

N2 - 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 (γ-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.

AB - 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 (γ-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.

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AN - SCOPUS:85055855595

SN - 0028-0836

VL - 563

SP - 72

EP - 78

JO - Nature

JF - Nature

IS - 7729

ER -

Shared and distinct transcriptomic cell types across neocortical areas

Abstract

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