Global profiling of prostate cancer cell expression upon treatment with media conditioned from human stromal cells ectopically expressing PDK4

Technical advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiles of human prostate cancer cell lines exposed to conditioned media from human primary stromal cells engineered to express pyruvate dehydrogenase kinase 4 (PDK4), a key enzyme that is correlated with glucose metabolism, negatively regulates the conversion of pyruvate to acetyl-CoA and plays important roles in cancer progression and multiple other pathological events. Overall design: Transcript profiles of prostate cancer cell lines mainly PC3, DU145 and M12 were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. 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.