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A Taxonomy of Transcriptomic Cell Types Across the Isocortex and Hippocampal Formation

75 Pages Posted: 28 Apr 2020 Sneak Peek Status: Review Complete

See all articles by Zizhen Yao

Zizhen Yao

Allen Institute for Brain Science

Thuc Nghi Nguyen

Allen Institute for Brain Science

Cindy T. J. van Velthoven

Allen Institute for Brain Science

Jeff Goldy

Allen Institute for Brain Science

Adriana E. Sedeno-Cortes

Allen Institute for Brain Science

Fahimeh Baftizadeh

Allen Institute for Brain Science

Darren Bertagnolli

Allen Institute for Brain Science

Tamara Casper

Allen Institute for Brain Science

Kirsten Crichton

Allen Institute for Brain Science

Song-Lin Ding

Allen Institute for Brain Science

Olivia Fong

Allen Institute for Brain Science

Emma Garren

Allen Institute for Brain Science

Alexandra Glandon

Allen Institute for Brain Science

James Gray

Allen Institute for Brain Science

Lucas T. Graybuck

Allen Institute for Brain Science

Michael J. Hawrylycz

Allen Institute for Brain Science

Daniel Hirschstein

Allen Institute for Brain Science

Matthew Kroll

Allen Institute for Brain Science

Kanan Lathia

Allen Institute for Brain Science

Boaz Levi

Allen Institute for Brain Science

Delissa McMillen

Allen Institute for Brain Science

Stephanie Mok

Allen Institute for Brain Science

Thanh Pham

Allen Institute for Brain Science

Qingzhong Ren

Allen Institute for Brain Science

Christine Rimorin

Allen Institute for Brain Science

Nadiya Shapovalova

Allen Institute for Brain Science

Josef Sulc

Allen Institute for Brain Science

Susan M. Sunkin

Allen Institute for Brain Science

Michael Tieu

Allen Institute for Brain Science

Amy Torkelson

Allen Institute for Brain Science

Herman Tung

Allen Institute for Brain Science

Katelyn Ward

Allen Institute for Brain Science

Nick Dee

Allen Institute for Brain Science

Kimberly A. Smith

Allen Institute for Brain Science

Bosiljka Tasic

Allen Institute for Brain Science

Hongkui Zeng

Allen Institute for Brain Science

More...

Abstract

The isocortex and hippocampal formation are two major structures in the mammalian brain that play critical roles in perception, cognition, emotion and learning. Using single-cell RNA-sequencing approaches, we profiled ~1.2 million cells covering all regions in the adult mouse isocortex and hippocampal formation. The cell types are organized hierarchically and exhibit varying degrees of discrete or continuous variations. Such molecular relationships correlate strongly with the spatial distribution patterns of the cell types, which can be region-specific, shared across multiple regions, or part of one or more gradients. Glutamatergic neuron types display much greater diversity than GABAergic neuron types, both molecularly and spatially, and define regional identities as well as inter-region relationships. Our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation for the first time, and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these two brain structures.

Keywords: single-cell RNA-sequencing, transcriptomic, cell types, taxonomy, neocortex, hippocampus, glutamatergic, GABAergic interneuron

Suggested Citation

Yao, Zizhen and Nguyen, Thuc Nghi and van Velthoven, Cindy T. J. and Goldy, Jeff and Sedeno-Cortes, Adriana E. and Baftizadeh, Fahimeh and Bertagnolli, Darren and Casper, Tamara and Crichton, Kirsten and Ding, Song-Lin and Fong, Olivia and Garren, Emma and Glandon, Alexandra and Gray, James and Graybuck, Lucas T. and Hawrylycz, Michael J. and Hirschstein, Daniel and Kroll, Matthew and Lathia, Kanan and Levi, Boaz and McMillen, Delissa and Mok, Stephanie and Pham, Thanh and Ren, Qingzhong and Rimorin, Christine and Shapovalova, Nadiya and Sulc, Josef and Sunkin, Susan M. and Tieu, Michael and Torkelson, Amy and Tung, Herman and Ward, Katelyn and Dee, Nick and Smith, Kimberly A. and Tasic, Bosiljka and Zeng, Hongkui, A Taxonomy of Transcriptomic Cell Types Across the Isocortex and Hippocampal Formation. Available at SSRN: https://ssrn.com/abstract=3575167 or http://dx.doi.org/10.2139/ssrn.3575167
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Zizhen Yao

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Thuc Nghi Nguyen

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Cindy T. J. Van Velthoven

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

Adriana E. Sedeno-Cortes

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

Darren Bertagnolli

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

Song-Lin Ding

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

Emma Garren

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

James Gray

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Lucas T. Graybuck

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

Daniel Hirschstein

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

Kanan Lathia

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Boaz Levi

Allen Institute for Brain Science ( email )

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

Stephanie Mok

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

Qingzhong Ren

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

Nadiya Shapovalova

Allen Institute for Brain Science

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

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

Herman Tung

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

Nick Dee

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

Kimberly A. Smith

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

Hongkui Zeng (Contact Author)

Allen Institute for Brain Science

615 Westlake Ave N
Seattle, WA 98109
United States

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