RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls.

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular and molecular pathways. The goals of this study are to compare NGS-derived Cere-120 treated SMG transcriptome profile (RNA-seq) to the AAV2-GFP and Non-IR SMGs Methods: SMG mRNA profiles of Non-IR, IR-GFP and Cere-120 treated mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays