Transcriptomic Reprogramming of Prostate Cancer Cells Driven by Stroma-Derived AREG

Recent advances in next generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways and responses. We performed this study to investigate the transcriptome profiling (RNA-seq) of prostate cancer cells upon in vitro treatment with the conditioned media from prostate stromal cells exogenously expressing human AREG. Overall transcript profiles of prostate cancer cell lines including PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10. 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 Green assays