Illumina HiSeq 2500 paired end sequencing; RNA-seq of the human HCC cell line PLC5 after 72 hours treatment with either MAGEA3 shRNA or Scramble control
PLC5 cells were infected with polybrene (8µg/ml) and lentiviruses expressing either an empty vector (pLKO.1) or a shRNA against MAGEA3 (pLKO.1) from Sigma-Aldrich: shMAGEA3 #8375: TRCN00000128375. Cells were collected 72 hours after infection and used for RNA extraction. Lentivirus was diluted 1:2 for the RNA sequencing experiment.    PLC5 cells were infected with polybrene (8µg/ml) and lentiviruses expressing either an empty vector (pLKO.1) or a shRNA against MAGEA3 (pLKO.1) from Sigma-Aldrich: shMAGEA3 #8375: TRCN00000128375. Cells were collected 72 hours after infection and used for RNA extraction. Lentivirus was diluted 1:2 for the RNA sequencing experiment.  RNA from cell lines was extracted using the RNeasy mini kit (Qiagen). Libraries were constructed using the TruSeq RNA Library Prep Kit v2.