GSE118645
BCL6 confers KRAS-mutant NSCLCs resistance to BET inhibitors
We report that OTX015 upregulates BCL6 in KRAS-mutant NSCLC cells. Considering that both BCL6 and BET proteins regulate target genes by affecting transcription, we performed an RNA-seq experiment to identify downstream genes which response to OTX015. Retinal mRNA profiles of A549 cells treated with DMSO (0.1% for 6 hr) and OTX015 (1 µM for 6 hr) were generated by deep sequencing, in triplicate, using the SOLiD v4 sequencing platform. 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. Overall design: Retinal mRNA profiles of A549 treated with 1µM OTX015 for 6 hr or not were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 sequencing platform.