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A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Authors :
Susan M. Sunkin
Qingzhong Ren
Michael Tieu
Fahimeh Baftizadeh
Kimberly A. Smith
Boaz P. Levi
Kanan Lathia
Olivia Fong
James Gray
Lucas T. Graybuck
Jeff Goldy
Bosiljka Tasic
Christine Rimorin
Thuc Nghi Nguyen
Kirsten Crichton
Josef Sulc
Songlin Ding
Darren Bertagnolli
Zizhen Yao
Hongkui Zeng
Delissa McMillen
Cindy T. J. van Velthoven
Katelyn Ward
Alexandra Glandon
Thanh Pham
Herman Tung
Amy Torkelson
Nick Dee
Nadiya V. Shapovalova
Stephanie Mok
Emma Garren
Matthew Kroll
Tamara Casper
Adriana E. Sedeno-Cortes
Daniel Hirschstein
Publication Year :
2020
Publisher :
Cold Spring Harbor Laboratory, 2020.

Abstract

SUMMARYThe isocortex and hippocampal formation are two major structures in the mammalian brain that play critical roles in perception, cognition, emotion and learning. Both structures contain multiple regions, for many of which the cellular composition is still poorly understood. In this study, we used two complementary single-cell RNA-sequencing approaches, SMART-Seq and 10x, to profile ∼1.2 million cells covering all regions in the adult mouse isocortex and hippocampal formation, and derived a cell type taxonomy comprising 379 transcriptomic types. The completeness of coverage enabled us to define gene expression variations across the entire spatial landscape without significant gaps. We found that cell types are organized in a hierarchical manner and exhibit varying degrees of discrete or continuous relatedness with each other. Such molecular relationships correlate strongly with the spatial distribution patterns of the cell types, which can be region-specific, or shared across multiple regions, or part of one or more gradients along with other cell types. Glutamatergic neuron types have much greater diversity than GABAergic neuron types, both molecularly and spatially, and they define regional identities as well as inter-region relationships. For example, we found that glutamatergic cell types between the isocortex and hippocampal formation are highly distinct from each other yet possess shared molecular signatures and corresponding layer specificities, indicating their homologous relationships. Overall, 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.

Details

Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....653919e9a1531a38cf23c9a9c7ff9701
Full Text :
https://doi.org/10.1101/2020.03.30.015214