library_construction_protocol: Total RNA was isolated with the Trizol reagent for MCF-7 cells and with the High Pure RNA isolation kit (Roche) for BT-474 and SK-BR-3 cells. RNA concentration was measured at the Nanodrop ND-1000 and RNA integrity was checked with the Bioanalyzer 2100 (Agilent). For MCF-7 cells, library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) starting from 1,000 ng of total RNA. For SK-BR-3 and BT-474 cells libraries for RNA-Seq were prepared with the NEBNext Ultra RNA II directional kit including NEBNext mRNA enrichment. RNA and library quality control was checked by TapeStation (Agilent).