Transcription analysis of cochlear development in minipigs

Abstract

Conclusions: The critical stage for cochlear gene regulation in the embryo is E49–E56. These data provide a valuable resource to help elucidate gene regulation in cochlear development and will benefit ear-related studies, especially those that focus on gene and stem cell therapies in hearing loss.

Objectives: To investigate gene regulation in cochlear development and provide reference information for ear-related research.

Methods: Total RNA extraction from the Bama miniature pig cochlea was performed at five time points that covered most of the cochlea development process (E42, E49, E56, E91, P13). Transcriptome sequencing was performed by Illumina HiSeq 2500. Transcriptome data were mapped to the genome using TopHat2. Gene expression was quantified using the Cuffquant and Cuffnorm modules. GO and KEGG pathway-enrichment analysis were in progress about the differentially expressed genes (DEGs) by Perl programs.

Results: Sequencing of 1778643560000 paired reads revealed 35.9 G of data, and 19,432 expression genes were detected. The ratio of these pairs to the Ensembl genome database was approximately 71% in all samples. The stages E49–E91 and, especially, E49–E56 included the most rapid changes in gene regulation and differentiation for the cochlea. The stem cell characteristics of neural stem cells decreased most rapidly during this period.

Chinese abstract

结论: 胚胎中耳蜗基因调控的关键期为E49-E56。这些数据提供了宝贵的资料, 来帮助阐明耳蜗发育中的基因调控, 并将有益于与耳朵相关的研究, 特别有益于用基因和干细胞治疗听力损失的研究。

目的: 调查耳蜗发育中的基因调控, 为耳研究提供参考信息。

方法: 在跨大部分巴马微型猪耳蜗发育过程的5个时点（E42, E49, E56, E91, P13）, 从耳蜗中提取总RNA。转录组测序用Illumina HiSeq 2500进行。使用TopHat2将转录组数据映射到基因组。使用Cuffquant和Cuffnorm模块来量化基因表达。我们正在用Perl程序对差异表达的基因（DEGs）进行GO和KEGG途径-富集分析。

结果: 1778643560000配对读数的测序展示35.9 G的数据量, 检测到19,432个表达基因。在所有样品中, 这些配对读数占Ensembl基因组数据库大约71％。阶段E49-E91, 特别是E49-E56, 包括着耳蜗的基因调节和分化的最快变化。在此期间, 神经干细胞的干细胞特征减少最快。

Keywords:

• Transcriptome analysis
• porcine
• cochlea development
• celloidin section

Additional information

Funding

This study was supported by the Major Scientific Problem-oriented Project under the National Key Basic Research Program (973 Program) (Grant No. 2011CBA01000), the National Basic Research Program of China (973 Program) (#2012CB967900), and the Natural Science Foundation of Jilin Province Science and Technology Department (20160101020JC), National Science and Technology Major Project of China (2014ZX08009-003-006), National Science and Technology Infrastructure Program of China (2012BAI39B04), Research start-up fund (20700223) and Fundamental Research Funds of Southwest University (No. XDJK2012C097).