RNA-seq of the human HCC cell line PLC5 after 72 hours treatment with either MAGEA3 shRNA or Scramble control

To better understand the mechanism by which MAGEA3 contributes to HCC progression, we conducted RNA sequencing in the PLC5 HCC cell line after 72 hours of treatment with scramble or sh8375 in triplicate. RNA-sequencing was conducted on poly-A enriched RNA, 100 bp single reads using an Illumina HiSeq2500 instrument. Libraries were constructed using the TruSeq RNA Library Prep Kit v2. Raw sequencing reads were mapped to the GRCh38 reference genome (USCS) using STAR (2.4.2g1). Aligned reads were mapped to GRCh38 genetic features using featureCounts from the subRead package with default settings. Data analysis included differential gene expression between conditions and gene set enrichment analysis.