Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NS-DADm mice myocardium Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived heart 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 Methods: myocardium mRNA profiles of 6-week-old wild-type (WT) and whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm) mice were generated by Agilent 2100 Bio analyzer. we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis andfunctional annotations Results: Using an optimized data analysis workflow, we find genes upregulated and enriched in NS-DADm myocardium that were consistent with HDAC3 inhibitor treated heart compared with WT Conclusions: Our study represents the first detailed analysis of genes expression in myocardium of HDAC3 enzymatic activity-dead NS-DADm mice Myocardium mRNA profiles of 6-week old wild type (WT) and NS-DADm mice