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

Callaway, EM (author)
Dong, HW (author)
Ecker, JR (author)
show more...
Hawrylycz, MJ (author)
Huang, ZJ (author)
Lein, ES (author)
Ngai, J (author)
Osten, P (author)
Ren, B (author)
Tolias, AS (author)
White, O (author)
Zeng, HK (author)
Zhuang, XW (author)
Ascoli, GA (author)
Behrens, MM (author)
Chun, J (author)
Feng, GP (author)
Gee, JC (author)
Ghosh, SS (author)
Halchenko, YO (author)
Hertzano, R (author)
Lim, BK (author)
Martone, ME (author)
Ng, L (author)
Pachter, L (author)
Ropelewski, AJ (author)
Tickle, TL (author)
Yang, XW (author)
Zhang, K (author)
Bakken, TE (author)
Berens, P (author)
Daigle, TL (author)
Harris, JA (author)
Jorstad, NL (author)
Kalmbach, BE (author)
Kobak, D (author)
Li, YE (author)
Liu, HQ (author)
Matho, KS (author)
Mukamel, EA (author)
Naeemi, M (author)
Scala, F (author)
Tan, PC (author)
Ting, JT (author)
Xie, FM (author)
Zhang, M (author)
Zhang, ZZ (author)
Zhou, JT (author)
Zingg, B (author)
Bertagnolli, D (author)
Casper, T (author)
Crichton, K (author)
Dee, N (author)
Diep, D (author)
Ding, SL (author)
Dong, WX (author)
Dougherty, EL (author)
Fong, O (author)
Goldman, M (author)
Goldy, J (author)
Hodge, RD (author)
Hu, LJ (author)
Keene, CD (author)
Krienen, FM (author)
Kroll, M (author)
Lake, BB (author)
Lathia, K (author)
Linnarsson, S (author)
Karolinska Institutet
Liu, CS (author)
Macosko, EZ (author)
McCarroll, SA (author)
McMillen, D (author)
Nadaf, NM (author)
Nguyen, TN (author)
Palmer, CR (author)
Pham, T (author)
Plongthongkum, N (author)
Reed, NM (author)
Regev, A (author)
Rimorin, C (author)
Romanow, WJ (author)
Savoia, S (author)
Siletti, K (author)
Smith, K (author)
Sulc, J (author)
Tasic, B (author)
Tieu, M (author)
Torkelson, A (author)
Tung, H (author)
van Velthoven, CTJ (author)
Vanderburg, CR (author)
Yanny, AM (author)
Fang, RX (author)
Hou, XM (author)
Lucero, JD (author)
Osteen, JK (author)
Pinto-Duarte, A (author)
Poirion, O (author)
Preissl, S (author)
Wang, XX (author)
Aldridge, AI (author)
Bartlett, A (author)
Boggeman, L (author)
O'Connor, C (author)
Castanon, RG (author)
Chen, HM (author)
Fitzpatrick, C (author)
Luo, CY (author)
Nery, JR (author)
Nunn, M (author)
Rivkin, AC (author)
Tian, W (author)
Dominguez, B (author)
Ito-Cole, T (author)
Jacobs, M (author)
Jin, X (author)
Lee, CT (author)
Lee, KF (author)
Miyazaki, PA (author)
Pang, Y (author)
Rashid, M (author)
Smith, JB (author)
Vu, M (author)
Williams, E (author)
Armand, E (author)
Biancalani, T (author)
Booeshaghi, AS (author)
Crow, M (author)
Dudoit, S (author)
Fischer, S (author)
Gillis, J (author)
Hu, QW (author)
Kharchenko, PV (author)
Niu, SY (author)
Ntranos, V (author)
Purdom, E (author)
Risso, D (author)
de Bezieux, HR (author)
Somasundaram, S (author)
Street, K (author)
Svensson, V (author)
Vaishnav, ED (author)
Van den Berge, K (author)
Welch, JD (author)
Yao, ZZ (author)
An, X (author)
Bateup, HS (author)
Bowman, I (author)
Chance, RK (author)
Foster, NN (author)
Galbavy, W (author)
Gong, H (author)
Gou, L (author)
Hatfield, JT (author)
Hintiryan, H (author)
Hirokawa, KE (author)
Kim, G (author)
Kramer, DJ (author)
Li, AA (author)
Li, XN (author)
Luo, QM (author)
Munoz-Castaneda, R (author)
Stafford, DA (author)
Feng, Z (author)
Jia, XY (author)
Jiang, SD (author)
Jiang, T (author)
Kuang, XL (author)
Larsen, R (author)
Lesnar, P (author)
Li, YY (author)
Li, YY (author)
Liu, LJ (author)
Peng, HC (author)
Qu, L (author)
Ren, M (author)
Ruan, ZC (author)
Shen, E (author)
Song, YY (author)
Wakeman, W (author)
Wang, P (author)
Wang, YM (author)
Wang, Y (author)
Yin, LL (author)
Yuan, J (author)
Zhao, SJ (author)
Zhao, X (author)
Narasimhan, A (author)
Palaniswamy, R (author)
Banerjee, S (author)
Ding, LY (author)
Huilgol, D (author)
Huo, BX (author)
Kuo, HC (author)
Laturnus, S (author)
Li, X (author)
Mitra, PP (author)
Mizrachi, J (author)
Wang, QX (author)
Xie, P (author)
Xiong, F (author)
Yu, Y (author)
Eichhorn, SW (author)
Berg, J (author)
Bernabucci, M (author)
Bernaerts, Y (author)
Cadwell, CR (author)
Castro, JR (author)
Dalley, R (author)
Hartmanis, L (author)
Karolinska Institutet
Horwitz, GD (author)
Jiang, XL (author)
Ko, AL (author)
Miranda, E (author)
Mulherkar, S (author)
Nicovich, PR (author)
Owen, SF (author)
Sandberg, R (author)
Karolinska Institutet
Sorensen, SA (author)
Tan, ZH (author)
Allen, S (author)
Hockemeyer, D (author)
Lee, AY (author)
Veldman, MB (author)
Adkins, RS (author)
Ament, SA (author)
Bravo, HC (author)
Carter, R (author)
Chatterjee, A (author)
Colantuoni, C (author)
Crabtree, J (author)
Creasy, H (author)
Felix, V (author)
Giglio, M (author)
Herb, BR (author)
Kancherla, J (author)
Mahurkar, A (author)
McCracken, C (author)
Nickel, L (author)
Olley, D (author)
Orvis, J (author)
Schor, M (author)
Hood, G (author)
Dichter, B (author)
Grauer, M (author)
Helba, B (author)
Bandrowski, A (author)
Barkas, N (author)
Carlin, B (author)
D'Orazi, FD (author)
Degatano, K (author)
Gillespie, TH (author)
Khajouei, F (author)
Konwar, K (author)
Thompson, C (author)
Kelly, K (author)
Mok, S (author)
Sunkin, S (author)
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 (creator_code:org_t)
2021-10-06
2021
English.
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
  • Journal article (peer-reviewed)
Abstract Subject headings
Close  
  • 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.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Neurovetenskaper (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Neurosciences (hsv//eng)
MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

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By the author/editor
Callaway, EM
Dong, HW
Ecker, JR
Hawrylycz, MJ
Huang, ZJ
Lein, ES
show more...
Ngai, J
Osten, P
Ren, B
Tolias, AS
White, O
Zeng, HK
Zhuang, XW
Ascoli, GA
Behrens, MM
Chun, J
Feng, GP
Gee, JC
Ghosh, SS
Halchenko, YO
Hertzano, R
Lim, BK
Martone, ME
Ng, L
Pachter, L
Ropelewski, AJ
Tickle, TL
Yang, XW
Zhang, K
Bakken, TE
Berens, P
Daigle, TL
Harris, JA
Jorstad, NL
Kalmbach, BE
Kobak, D
Li, YE
Liu, HQ
Matho, KS
Mukamel, EA
Naeemi, M
Scala, F
Tan, PC
Ting, JT
Xie, FM
Zhang, M
Zhang, ZZ
Zhou, JT
Zingg, B
Bertagnolli, D
Casper, T
Crichton, K
Dee, N
Diep, D
Ding, SL
Dong, WX
Dougherty, EL
Fong, O
Goldman, M
Goldy, J
Hodge, RD
Hu, LJ
Keene, CD
Krienen, FM
Kroll, M
Lake, BB
Lathia, K
Linnarsson, S
Liu, CS
Macosko, EZ
McCarroll, SA
McMillen, D
Nadaf, NM
Nguyen, TN
Palmer, CR
Pham, T
Plongthongkum, N
Reed, NM
Regev, A
Rimorin, C
Romanow, WJ
Savoia, S
Siletti, K
Smith, K
Sulc, J
Tasic, B
Tieu, M
Torkelson, A
Tung, H
van Velthoven, C ...
Vanderburg, CR
Yanny, AM
Fang, RX
Hou, XM
Lucero, JD
Osteen, JK
Pinto-Duarte, A
Poirion, O
Preissl, S
Wang, XX
Aldridge, AI
Bartlett, A
Boggeman, L
O'Connor, C
Castanon, RG
Chen, HM
Fitzpatrick, C
Luo, CY
Nery, JR
Nunn, M
Rivkin, AC
Tian, W
Dominguez, B
Ito-Cole, T
Jacobs, M
Jin, X
Lee, CT
Lee, KF
Miyazaki, PA
Pang, Y
Rashid, M
Smith, JB
Vu, M
Williams, E
Armand, E
Biancalani, T
Booeshaghi, AS
Crow, M
Dudoit, S
Fischer, S
Gillis, J
Hu, QW
Kharchenko, PV
Niu, SY
Ntranos, V
Purdom, E
Risso, D
de Bezieux, HR
Somasundaram, S
Street, K
Svensson, V
Vaishnav, ED
Van den Berge, K
Welch, JD
Yao, ZZ
An, X
Bateup, HS
Bowman, I
Chance, RK
Foster, NN
Galbavy, W
Gong, H
Gou, L
Hatfield, JT
Hintiryan, H
Hirokawa, KE
Kim, G
Kramer, DJ
Li, AA
Li, XN
Luo, QM
Munoz-Castaneda, ...
Stafford, DA
Feng, Z
Jia, XY
Jiang, SD
Jiang, T
Kuang, XL
Larsen, R
Lesnar, P
Li, YY
Liu, LJ
Peng, HC
Qu, L
Ren, M
Ruan, ZC
Shen, E
Song, YY
Wakeman, W
Wang, P
Wang, YM
Wang, Y
Yin, LL
Yuan, J
Zhao, SJ
Zhao, X
Narasimhan, A
Palaniswamy, R
Banerjee, S
Ding, LY
Huilgol, D
Huo, BX
Kuo, HC
Laturnus, S
Li, X
Mitra, PP
Mizrachi, J
Wang, QX
Xie, P
Xiong, F
Yu, Y
Eichhorn, SW
Berg, J
Bernabucci, M
Bernaerts, Y
Cadwell, CR
Castro, JR
Dalley, R
Hartmanis, L
Horwitz, GD
Jiang, XL
Ko, AL
Miranda, E
Mulherkar, S
Nicovich, PR
Owen, SF
Sandberg, R
Sorensen, SA
Tan, ZH
Allen, S
Hockemeyer, D
Lee, AY
Veldman, MB
Adkins, RS
Ament, SA
Bravo, HC
Carter, R
Chatterjee, A
Colantuoni, C
Crabtree, J
Creasy, H
Felix, V
Giglio, M
Herb, BR
Kancherla, J
Mahurkar, A
McCracken, C
Nickel, L
Olley, D
Orvis, J
Schor, M
Hood, G
Dichter, B
Grauer, M
Helba, B
Bandrowski, A
Barkas, N
Carlin, B
D'Orazi, FD
Degatano, K
Gillespie, TH
Khajouei, F
Konwar, K
Thompson, C
Kelly, K
Mok, S
Sunkin, S
show less...
About the subject
MEDICAL AND HEALTH SCIENCES
MEDICAL AND HEAL ...
and Basic Medicine
and Neurosciences
MEDICAL AND HEALTH SCIENCES
MEDICAL AND HEAL ...
and Basic Medicine
and Medical Genetics
Articles in the publication
Nature
By the university
Karolinska Institutet

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