Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages

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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.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE132925.

The following data sets were generated

1. Li C
2. Li X
3. Bi Z
4. Sugino K
5. Wang G
6. Zhu T
7. Liu Z
(2019) RNA-Seq of mouse inner ear SGNs, HCs and Glias
NCBI Gene Expression Omnibus, GSE132925.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132925

Article and author information

Author details

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.
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.
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.
Ken Sugino

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5795-0635
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.
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.
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.

"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.

Copyright

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.