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. 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.