Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells

In the paper "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we identified Fra-1 and/or Fra-2 target genes in MDA-MB-231 cells. si RNA against Fra-1 and against Fra-2 were transfected in MDA-MB-231 cells either independenlty or simultaneously to identify genes regulated specifically by Fra-1 or Fra-2 and genes regulated redundantly or complementarily by Fra-1 and Fra-2 total RNA were purified and biotinylated sense-strand cDNA were produced. cDNA targets were used to probe Affymetrix GeneChip Human Gene 2.0 ST arrays transcriptome 1 : cells either non transfected (T1.NT) or transfected with control siRNA (T1.siCTL) , siRNA against Fra-1 (T.siFra1) or against Fra-2 (T1.siFra2). 3 independant replicates (A, B and C) for each condition were produced transcriptome 2 : cells either non transfected (T2.NT) or transfected with control siRNA (T2.siCTL) , with siRNA against Fra-1 + siRNA against Fra-2 (T2.siFra1_siFra2). 3 independant replicates (A, B and C) for each condition were produced to discard bias linked to siRNA transfection itself, as well as potential bias linked to control siRNA , we introduced another control, i.e. cells that received the transfection reagent but not transfected (NT) with siRNA. Fold changes were calculated versus NT conditions for the different siRNA transfections