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

52 Pages Posted: 30 Mar 2020 Sneak Peek Status: Review Complete

See all articles by Nathan W. Gouwens

Nathan W. Gouwens

Allen Institute for Brain Science

Staci A. Sorensen

Allen Institute for Brain Science

Fahimeh Baftizadeh

Allen Institute for Brain Science

Agata Budzillo

Allen Institute for Brain Science

Brian R. Lee

Allen Institute for Brain Science

Tim Jarsky

Allen Institute for Brain Science

Lauren Alfiler

Allen Institute for Brain Science

Katherine Baker

Allen Institute for Brain Science

Eliza Barkan

Allen Institute for Brain Science

Kyla Berry

Allen Institute for Brain Science

Darren Bertagnolli

Allen Institute for Brain Science

Kris Bickley

Allen Institute for Brain Science

Jasmine Bomben

Allen Institute for Brain Science

Thomas Braun

Allen Institute for Brain Science

Kirssy Brouner

Allen Institute for Brain Science

Tamara Casper

Allen Institute for Brain Science

Kirsten Crichton

Allen Institute for Brain Science

Tanya L. Daigle

Allen Institute for Brain Science

Rachel Dalley

Allen Institute for Brain Science

Rebeeca de Frates

Allen Institute for Brain Science

Nick Dee

Allen Institute for Brain Science

Tsega Desta

Allen Institute for Brain Science

Samuel Dingman Lee

Allen Institute for Brain Science

Nadezhda Dotson

Allen Institute for Brain Science

Tom Egdorf

Allen Institute for Brain Science

Lauren Ellingwood

Allen Institute for Brain Science

Rachel Enstrom

Allen Institute for Brain Science

Luke Esposito

Allen Institute for Brain Science

Colin Farrell

Allen Institute for Brain Science

David Feng

Allen Institute for Brain Science

Olivia Fong

Allen Institute for Brain Science

Rohan Gala

Allen Institute for Brain Science

Clare Gamlin

Allen Institute for Brain Science

Amanda Gary

Allen Institute for Brain Science

Alexandra Glandon

Allen Institute for Brain Science

Jeff Goldy

Allen Institute for Brain Science

Melissa Gorham

Allen Institute for Brain Science

Lucas Graybuck

Allen Institute for Brain Science

Hong Gu

Allen Institute for Brain Science

Kirsten Hadley

Allen Institute for Brain Science

Michael J. Hawrylycz

Allen Institute for Brain Science

Alex M. Henry

Allen Institute for Brain Science

DiJon Hill

Allen Institute for Brain Science

Madie Happ

Allen Institute for Brain Science

Sara Kebede

Allen Institute for Brain Science

Tae Kyung Kim

Allen Institute for Brain Science

Lisa Kim

Allen Institute for Brain Science

Matthew Kroll

Allen Institute for Brain Science

Changkyu Lee

Allen Institute for Brain Science

Katherine E. Link

Allen Institute for Brain Science

Matthew Mallory

Allen Institute for Brain Science

Rusty Mann

Allen Institute for Brain Science

Michelle Maxwell

Allen Institute for Brain Science

Medea McGraw

Allen Institute for Brain Science

Delissa McMillen

Allen Institute for Brain Science

Alice Mukora

Allen Institute for Brain Science

Lindsay Ng

Allen Institute for Brain Science

Lydia Ng

Allen Institute for Brain Science

Kiet Ngo

Allen Institute for Brain Science

Philip R. Nicovich

Allen Institute for Brain Science

Aaron Oldre

Allen Institute for Brain Science

Daniel Park

Allen Institute for Brain Science

Hanchuan Peng

Allen Institute for Brain Science

Osnat Penn

Allen Institute for Brain Science

Thanh Pham

Allen Institute for Brain Science

Alice Pom

Allen Institute for Brain Science

Lyida Potekhina

Allen Institute for Brain Science

Ramkumar Rajanbabu

Allen Institute for Brain Science

Shea Ransford

Allen Institute for Brain Science

David Reid

Allen Institute for Brain Science

Christine Rimorin

Allen Institute for Brain Science

Miranda Robertson

Allen Institute for Brain Science

Kara Ronellenfitch

Allen Institute for Brain Science

Augustin Ruiz

Allen Institute for Brain Science

David Sandman

Allen Institute for Brain Science

Kimberly Smith

Allen Institute for Brain Science

Josef Sulc

Allen Institute for Brain Science

Susan M. Sunkin

Allen Institute for Brain Science

Aaron Szafer

Allen Institute for Brain Science

Michael Tieu

Allen Institute for Brain Science

Amy Torkelson

Allen Institute for Brain Science

Jessica Trinh

Allen Institute for Brain Science

Herman Tung

Allen Institute for Brain Science

Wayne Wakeman

Allen Institute for Brain Science

Katelyn Ward

Allen Institute for Brain Science

Grace Williams

Allen Institute for Brain Science

Zhi Zhou

Allen Institute for Brain Science

Jonathan Ting

Allen Institute for Brain Science

Anton Arkhipov

Allen Institute for Brain Science

Uygar Sumbul

Allen Institute for Brain Science

Ed Lein

Allen Institute for Brain Science

Christof Koch

Allen Institute for Brain Science

Zizhen Yao

Allen Institute for Brain Science

Bosiljka Tasic

Allen Institute for Brain Science

Jim Berg

Allen Institute for Brain Science

Gabe J. Murphy

Allen Institute for Brain Science

Hongkui Zeng

Allen Institute for Brain Science

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Abstract

Neurons are frequently classified into distinct groups or cell types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 3,700 GABAergic mouse visual cortical neurons and reconstructed the local morphologies of 350 of those neurons. We found that most transcriptomic types (t-types) occupy specific laminar positions within mouse visual cortex, and many of those t-types exhibit consistent electrophysiological and morphological features. We observed that these properties could vary continuously between t- types, which limited the ability to predict specific t-types from other data modalities. Despite that, the data support the presence of at least 20 interneuron met-types that have congruent morphological, electrophysiological, and transcriptomic properties.

Keywords: GABAergic interneurons, somatostatin, parvalbumin, neuronal cell type, transcriptomics, taxonomy, Patch- seq, multimodal, visual cortex

Suggested Citation

Gouwens, Nathan W. and Sorensen, Staci A. and Baftizadeh, Fahimeh and Budzillo, Agata and Lee, Brian R. and Jarsky, Tim and Alfiler, Lauren and Baker, Katherine and Barkan, Eliza and Berry, Kyla and Bertagnolli, Darren and Bickley, Kris and Bomben, Jasmine and Braun, Thomas and Brouner, Kirssy and Casper, Tamara and Crichton, Kirsten and Daigle, Tanya L. and Dalley, Rachel and de Frates, Rebeeca and Dee, Nick and Desta, Tsega and Dingman Lee, Samuel and Dotson, Nadezhda and Egdorf, Tom and Ellingwood, Lauren and Enstrom, Rachel and Esposito, Luke and Farrell, Colin and Feng, David and Fong, Olivia and Gala, Rohan and Gamlin, Clare and Gary, Amanda and Glandon, Alexandra and Goldy, Jeff and Gorham, Melissa and Graybuck, Lucas and Gu, Hong and Hadley, Kirsten and Hawrylycz, Michael J. and Henry, Alex M. and Hill, DiJon and Happ, Madie and Kebede, Sara and Kyung Kim, Tae and Kim, Lisa and Kroll, Matthew and Lee, Changkyu and Link, Katherine E. and Mallory, Matthew and Mann, Rusty and Maxwell, Michelle and McGraw, Medea and McMillen, Delissa and Mukora, Alice and Ng, Lindsay and Ng, Lydia and Ngo, Kiet and Nicovich, Philip R. and Oldre, Aaron and Park, Daniel and Peng, Hanchuan and Penn, Osnat and Pham, Thanh and Pom, Alice and Potekhina, Lyida and Rajanbabu, Ramkumar and Ransford, Shea and Reid, David and Rimorin, Christine and Robertson, Miranda and Ronellenfitch, Kara and Ruiz, Augustin and Sandman, David and Smith, Kimberly and Sulc, Josef and Sunkin, Susan M. and Szafer, Aaron and Tieu, Michael and Torkelson, Amy and Trinh, Jessica and Tung, Herman and Wakeman, Wayne and Ward, Katelyn and Williams, Grace and Zhou, Zhi and Ting, Jonathan and Arkhipov, Anton and Sumbul, Uygar and Lein, Ed and Koch, Christof and Yao, Zizhen and Tasic, Bosiljka and Berg, Jim and Murphy, Gabe J. and Zeng, Hongkui, Toward an Integrated Classification of Cell Types: Morphoelectric and Transcriptomic Characterization of Individual GABAergic Cortical Neurons. Available at SSRN: https://ssrn.com/abstract=3544405 or http://dx.doi.org/10.2139/ssrn.3544405
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Nathan W. Gouwens

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Staci A. Sorensen

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Fahimeh Baftizadeh

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Agata Budzillo

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Brian R. Lee

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tim Jarsky

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lauren Alfiler

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Katherine Baker

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Eliza Barkan

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kyla Berry

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Darren Bertagnolli

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kris Bickley

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Jasmine Bomben

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Thomas Braun

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kirssy Brouner

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tamara Casper

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kirsten Crichton

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tanya L. Daigle

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Rachel Dalley

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Rebeeca De Frates

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Nick Dee

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tsega Desta

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Samuel Dingman Lee

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Nadezhda Dotson

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tom Egdorf

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lauren Ellingwood

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Rachel Enstrom

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Luke Esposito

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Colin Farrell

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

David Feng

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Olivia Fong

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Rohan Gala

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Clare Gamlin

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Amanda Gary

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Alexandra Glandon

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Jeff Goldy

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Melissa Gorham

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lucas Graybuck

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Hong Gu

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kirsten Hadley

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Michael J. Hawrylycz

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Alex M. Henry

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

DiJon Hill

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Madie Happ

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Sara Kebede

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Tae Kyung Kim

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lisa Kim

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Matthew Kroll

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Changkyu Lee

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Katherine E. Link

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Matthew Mallory

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Rusty Mann

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Michelle Maxwell

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Medea McGraw

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Delissa McMillen

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Alice Mukora

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lindsay Ng

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lydia Ng

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kiet Ngo

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Philip R. Nicovich

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Aaron Oldre

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Daniel Park

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Hanchuan Peng

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Osnat Penn

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Thanh Pham

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Alice Pom

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lyida Potekhina

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Ramkumar Rajanbabu

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Shea Ransford

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

David Reid

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Christine Rimorin

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Miranda Robertson

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kara Ronellenfitch

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Augustin Ruiz

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

David Sandman

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kimberly Smith

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Josef Sulc

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Susan M. Sunkin

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Aaron Szafer

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Michael Tieu

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Amy Torkelson

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Jessica Trinh

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Herman Tung

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Wayne Wakeman

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Katelyn Ward

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Grace Williams

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Zhi Zhou

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Jonathan Ting

Allen Institute for Brain Science

Anton Arkhipov

Allen Institute for Brain Science ( email )

615 Westlake Ave N
Seattle, WA 98109
United States

Uygar Sumbul

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Ed Lein

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Christof Koch

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Zizhen Yao

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Bosiljka Tasic

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Jim Berg

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Gabe J. Murphy (Contact Author)

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Hongkui Zeng

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

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