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Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages

  1. Chao Li
  2. Xiang Li
  3. Zhenghong Bi
  4. Ken Sugino
  5. Guangqin Wang
  6. Tong Zhu
  7. Zhiyong Liu  Is a corresponding author
  1. Chinese Academy of Sciences, China
  2. Janelia Research Campus, Howard Hughes Medical Institute, United States
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Cite this article as: eLife 2020;9:e50491 doi: 10.7554/eLife.50491

Abstract

Inner ear cochlear spiral ganglion neurons (SGNs) transmit auditory information to the brainstem. Recent single cell RNA-Seq studies have revealed heterogeneities within SGNs. Nonetheless, much remains unknown about the transcriptome of SGNs, especially which genes are specifically expressed in SGNs. To address these questions we needed a deeper and broader gene coverage than that in previous studies. We performed bulk RNA-Seq on mouse SGNs at five ages, and on two reference cell types (hair cells and glia). Their transcriptome comparison identified genes previously unknown to be specifically expressed in SGNs. To validate our dataset and provide useful genetic tools for this research field, we generated two knockin mouse strains: Scrt2-P2A-tdTomato and Celf4-3xHA-P2A-iCreER-T2A-EGFP. Our comprehensive analysis confirmed the SGN-selective expression of the candidate genes, testifying to the quality of our transcriptome data. These two mouse strains can be used to temporally label SGNs or to sort them.

Article and author information

Author details

  1. Chao Li

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Xiang Li

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Zhenghong Bi

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Ken Sugino

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5795-0635
  5. Guangqin Wang

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Tong Zhu

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Zhiyong Liu

    Institute of Neuroscience, State Key Laboratory of Neuroscience,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
    For correspondence
    zhiyongliu@ion.ac.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9675-1233

Funding

Ministry of Science and Technology of the People's Republic of China (2017YFA0103901)

  • Zhiyong Liu

Chinese Academy of Sciences (XDB32060100)

  • Zhiyong Liu

National Natural Science Foundation of China (81771012)

  • Zhiyong Liu

Shanghai Municipal Education Commission (2018SHZDZX05)

  • Zhiyong Liu

Boehringer Ingelheim (DE811138149)

  • Zhiyong Liu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mice were bred and raised in SPF level animal rooms and animal procedures were performed according to guidelines (NA-032-2019) of the IACUC of Institute of Neuroscience (ION), Chinese Academy of Sciences.

Reviewing Editor

  1. Tanya T Whitfield, University of Sheffield, United Kingdom

Publication history

  1. Received: July 24, 2019
  2. Accepted: January 7, 2020
  3. Accepted Manuscript published: January 8, 2020 (version 1)

Copyright

© 2020, Li et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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