Next Generation Sequencing Facilitates Quantitative Analysis of control, NDEA, NDEA + CFT-1 and NDEA+FYT Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between treatment and control model samples. Results: Using the RNA-seq analysis workflow, we mapped about an average of 80 million sequence reads per sample to the rat genome (Rnor_6.0) and identified 34,194 transcripts. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Male Wistar rats (N = 48, 140-160 g) were housed in a specific pathogen-free animal room and maintained under standard experimental conditions: temperature 22 ± 1 °C, relative humidity 50±10% with a 12 h light/dark cycle. After 1 week quarantine, the rats were randomized into 4 groups (N = 12/group): normal control group (Control group, intraperitoneal injection of 0.9% saline solution twice a week from 2-9th weeks and drink water), model controls group (NDEA group, intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks and drink water), CFT-1-treated group (NDEA + CFT-1, treated with Camellia sinensis (L.) O. Kuntze cv. CFT-1 tea infusion rich in epigallocatechin-3-gallate for 20 weeks and intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks), FYT-treated group (NDEA + FYT, treated with common tea Fuyun6 green tea infusion for 20 weeks and intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks). The feed, water, tea infusion intake and body weights were measured weekly. After 20 weeks, the rats were anesthetized by intraperitoneal injection of pentobarbital sodium (40 mg/kg) for collection of liver samples. Three liver samples were randomly selected from each group and stored at -80C for RNA sequencing.