Effect of the BET inhibitor, JQ1, on gene expression in triple-negative breast cancer cell lines. Homo sapiens

To study the effect of BET inhibition on gene expression in triple-negative breast cancer cells, we treated MDA-MB-231 and HCC70 cells with vehicle or the prototypical BET inhibitor, JQ1, for 72 hours. By comparing the expression profiles of vehicle-treated versus JQ1-treated cells, we can identify genes that respond to BET inhibition. The Affymetrix Human Gene 2.0. St Microarray were processed with RMA (robust multichip average algorithm) as implemented in Bioconductor package oligo, where background subtraction, quantile normalization and summarization (via median-polish) was accomplished. The top differentially expressed genes were identified using empirical Bayesian procedure of limma package. FDR method was selected to adjust the p-values for multiple testing. Overall design: MDA-MB-231 and HCC70 cells were treated with 0.1% DMSO or 500 nM JQ1 for 72 hours followed by RNA isolation