Transcription analysis of cochlear development in minipigs.

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.