Classification of electrophysiological and morphological neuron types in the mouse visual cortex.
Nathan W. Gouwens,Staci A. Sorensen,Jim Berg,Changkyu Lee,Tim Jarsky,Jonathan T. Ting,Susan M. Sunkin,David Feng,Costas A. Anastassiou,Eliza Barkan,Kris Bickley,Nicole Blesie,Thomas Braun,Krissy Brouner,Agata Budzillo,Shiella Caldejon,Tamara Casper,Dan Castelli,Peter Chong,Kirsten Crichton,Christine Cuhaciyan,Tanya L. Daigle,Rachel A. Dalley,Nick Dee,Tsega Desta,Songlin Ding,Samuel Dingman,Alyse Doperalski,Nadezhda Dotson,Tom Egdorf,Michael S. Fisher,Rebecca de Frates,Emma Garren,Marissa Garwood,Amanda Gary,Nathalie Gaudreault,Keith B. Godfrey,Melissa Gorham,Hong Gu,Caroline Habel,Kristen Hadley,James Harrington,Julie A. Harris,Alex M. Henry,DiJon Hill,Samuel R Josephsen,Sara Kebede,Lisa Kim,Matthew Kroll,Brian Lee,Tracy Lemon,Katherine E. Link,Xiaoxiao Liu,Brian Long,Rusty Mann,Medea McGraw,Stefan Mihalas,Alice Mukora,Gabe J. Murphy,Lindsay Ng,Kiet Ngo,Thuc Nghi Nguyen,Philip R. Nicovich,Aaron Oldre,Daniel Park,Sheana Parry,Jed Perkins,Lydia Potekhina,David Reid,Miranda Robertson,David Sandman,Martin Schroedter,Cliff Slaughterbeck,Gilberto J. Soler-Llavina,Josef Sulc,Aaron Szafer,Bosiljka Tasic,Naz Taskin,Corinne Teeter,Nivretta Thatra,Herman Tung,Wayne Wakeman,Grace Williams,Rob Young,Zhi Zhou,Colin Farrell,Hanchuan Peng,Michael Hawrylycz,Ed Lein,Lydia Ng,Anton Arkhipov,Amy Bernard,John W. Phillips,Hongkui Zeng,Christof Koch +94 more
TLDR
A single-cell characterization pipeline is established using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions to establish a morpho-electrical taxonomy of cell types for the mouse visual cortex via unsupervised clustering analysis of multiple quantitative features.Abstract:
Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets. Intrinsic physiological properties were measured from 1,938 neurons from the adult laboratory mouse visual cortex, morphological properties were measured from 461 reconstructed neurons, and 452 neurons had both measurements available. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We established a taxonomy of morphologically and electrophysiologically defined cell types for this region of the cortex, with 17 electrophysiological types, 38 morphological types and 46 morpho-electric types. There was good correspondence with previously defined transcriptomic cell types and subclasses using the same transgenic mouse lines.read more
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Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells.
Nathan W. Gouwens,Staci A. Sorensen,Fahimeh Baftizadeh,Agata Budzillo,Brian Lee,Tim Jarsky,Lauren Alfiler,Katherine Baker,Eliza Barkan,Kyla Berry,Darren Bertagnolli,Kris Bickley,Jasmine Bomben,Thomas Braun,Krissy Brouner,Tamara Casper,Kirsten Crichton,Tanya L. Daigle,Rachel A. Dalley,Rebecca de Frates,Nick Dee,Tsega Desta,Samuel Dingman Lee,Nadezhda Dotson,Tom Egdorf,Lauren Ellingwood,Rachel Enstrom,Luke Esposito,Colin Farrell,David Feng,Olivia Fong,Rohan Gala,Clare Gamlin,Amanda Gary,Alexandra Glandon,Jeff Goldy,Melissa Gorham,Lucas T. Graybuck,Hong Gu,Kristen Hadley,Michael Hawrylycz,Alex M. Henry,DiJon Hill,Madie Hupp,Sara Kebede,Tae Kyung Kim,Lisa Kim,Matthew Kroll,Changkyu Lee,Katherine E. Link,Matthew Mallory,Rusty Mann,Michelle Maxwell,Medea McGraw,Delissa McMillen,Alice Mukora,Lindsay Ng,Lydia Ng,Kiet Ngo,Philip R. Nicovich,Aaron Oldre,Daniel Park,Hanchuan Peng,Osnat Penn,Thanh Pham,Alice Pom,Zoran Popović,Lydia Potekhina,Ramkumar Rajanbabu,Shea Ransford,David Reid,Christine Rimorin,Miranda Robertson,Kara Ronellenfitch,Augustin Ruiz,David Sandman,Kimberly A. Smith,Josef Sulc,Susan M. Sunkin,Aaron Szafer,Michael Tieu,Amy Torkelson,Jessica Trinh,Herman Tung,Wayne Wakeman,Katelyn Ward,Grace Williams,Zhi Zhou,Jonathan T. Ting,Anton Arkhipov,Uygar Sümbül,Ed S. Lein,Christof Koch,Zizhen Yao,Bosiljka Tasic,Jim Berg,Gabe J. Murphy,Hongkui Zeng +97 more
TL;DR: 28 met- types are defined that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability, and layer-specific axon innervation pattern is identified as a defining feature distinguishing different met-types.
Journal ArticleDOI
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Trygve E. Bakken,Nikolas L. Jorstad,Qiwen Hu,Blue B. Lake,Wei Tian,Brian E. Kalmbach,Brian E. Kalmbach,Megan Crow,Rebecca D. Hodge,Fenna M. Krienen,Staci A. Sorensen,Jeroen Eggermont,Zizhen Yao,Brian D. Aevermann,Andrew Aldridge,Anna Bartlett,Darren Bertagnolli,Tamara Casper,Rosa Castanon,Kirsten Crichton,Tanya L. Daigle,Rachel A. Dalley,Nick Dee,Nikolai C. Dembrow,Nikolai C. Dembrow,Dinh Diep,Songlin Ding,Weixiu Dong,Rongxin Fang,Stephan Fischer,Melissa Goldman,Jeff Goldy,Lucas T. Graybuck,Brian R. Herb,Xiaomeng Hou,Jayaram Kancherla,Matthew Kroll,Kanan Lathia,Baldur van Lew,Yang Eric Li,Yang Eric Li,Christine S. Liu,Christine S. Liu,Hanqing Liu,Jacinta Lucero,Anup Mahurkar,Delissa McMillen,Jeremy A. Miller,Marmar Moussa,Joseph R. Nery,Philip R. Nicovich,Sheng-Yong Niu,Sheng-Yong Niu,Joshua Orvis,Julia K. Osteen,Scott F. Owen,C. Palmer,C. Palmer,Thanh Pham,Nongluk Plongthongkum,Olivier Poirion,Nora Reed,Christine Rimorin,Angeline Rivkin,William J. Romanow,Adriana E. Sedeno-Cortes,Kimberly Siletti,Saroja Somasundaram,Josef Sulc,Michael Tieu,Amy Torkelson,Herman Tung,Xinxin Wang,Fangming Xie,Anna Marie Yanny,Renee Zhang,Seth A. Ament,M. Margarita Behrens,Héctor Corrada Bravo,Jerold Chun,Alexander Dobin,Jesse Gillis,Ronna Hertzano,Patrick R. Hof,Thomas Höllt,Gregory D. Horwitz,C. Dirk Keene,Peter V. Kharchenko,Andrew L. Ko,Andrew L. Ko,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Chongyuan Luo,Eran A. Mukamel,Antonio Pinto-Duarte,Sebastian Preissl,Aviv Regev,Bing Ren,Bing Ren,Richard H. Scheuermann,Richard H. Scheuermann,Richard H. Scheuermann,Kimberly A. Smith,William J. Spain,William J. Spain,Owen White,Christof Koch,Michael Hawrylycz,Bosiljka Tasic,Evan Z. Macosko,Steven A. McCarroll,Steven A. McCarroll,Jonathan T. Ting,Jonathan T. Ting,Hongkui Zeng,Kun Zhang,Guoping Feng,Guoping Feng,Guoping Feng,Joseph R. Ecker,Sten Linnarsson,Ed S. Lein +121 more
TL;DR: The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals using high-throughput transcriptomic and epigenomic profiling of more than 450k single nuclei in humans, marmoset monkeys and mice as mentioned in this paper.
Journal ArticleDOI
Development and Arealization of the Cerebral Cortex.
Cathryn R. Cadwell,Aparna Bhaduri,Mohammed A. Mostajo-Radji,Matthew G. Keefe,Tomasz J. Nowakowski +4 more
TL;DR: This work proposes an integrated model of serial homology whereby intrinsic genetic programs and local factors establish early transcriptomic differences between excitatory neurons destined to give rise to broad "proto-regions," and activity-dependent mechanisms lead to progressive refinement and formation of sharp boundaries between functional areas.
Journal ArticleDOI
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Federico Scala,Dmitry Kobak,Matteo Bernabucci,Yves Bernaerts,Cathryn R. Cadwell,Jesus Ramon Castro,Leonard Hartmanis,Xiaolong Jiang,Sophie Laturnus,Elanine Miranda,Shalaka Mulherkar,Zheng Huan Tan,Zizhen Yao,Hongkui Zeng,Rickard Sandberg,Philipp Berens,Andreas S. Tolias +16 more
TL;DR: The results suggest that neuronal types in the neocortex do not always form discrete entities, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
Journal ArticleDOI
The diversity of GABAergic neurons and neural communication elements
TL;DR: It is posited that cardinal interneuron types can be defined by their synaptic communication properties, which are encoded in key transcriptional signatures, and a framework in which cell types are transcriptionally defined communication elements with characteristic input–output properties is proposed.
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