Next Generation Sequencing Facilitates Quantitative Analysis of overexpression of KLF14 in mouse primary hepatocytes and control cells

Purpose: KLF14 gene is closely linked to the development of Type 2 diabetes. The goals of this study are to compare KLF14-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Overall design: Methods:total RNA from the mouse primary hepatocytes, infected with the adenovirus carrying KLF14 expression vector or the empty vector was utilized for RNAseq to assess the global gene expression Retinal mRNA profiles were generated by deep sequencing, in triplicate. 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 TaqMan and SYBR Green assays