Transcriptome profiling (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549.

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) of wild type and MYOCD overexpression in human lung cancer cell line A549. Methods: mRNA profiles of wild type(WT) and MYOCD overexpression (MYOCD) human lung cancer cell line A549 were generated by deep sequencing, 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 TaqMan and SYBR. Overall design: mRNA profiles of human lung cancer cell line A549 with no treatment (WT) and MYOCD overexpression (MYOCD) were generated by deep sequencing using Illumina HiSeq 4000.研究目的：下一代测序（Next-generation sequencing, NGS）彻底变革了细胞通路的系统生物学分析。本研究旨在对比人肺癌细胞系A549中野生型与MYOCD过表达样本的转录组测序（transcriptome profiling, RNA-seq）数据。 研究方法：本研究通过深度测序，采用Illumina GAIIx平台，获取野生型（WT）与MYOCD过表达组（MYOCD）的人肺癌细胞系A549的mRNA表达谱。对通过质量过滤的测序读段，采用两种方法在转录本异构体水平开展分析：Burrows-Wheeler比对工具（Burrows–Wheeler Aligner, BWA）结合方差分析（ANOVA），以及TopHat与Cufflinks联用。此外，采用TaqMan探针法与SYBR染料法完成qRT-PCR验证。 整体实验设计：采用Illumina HiSeq 4000平台进行深度测序，获取未处理的野生型（WT）与MYOCD过表达组（MYOCD）的人肺癌细胞系A549的mRNA表达谱。