Towards resolution of the intron retention paradox in breast cancer

We explored intron retention patterns in normal breast epithelial cells (MCF10A) and estrogen receptor positive (ER+) breast cancer cells (MCF7). Overall design: Total RNA was isolated from MCF7 and MCF10A cells using Trizol (Invitrogen). The RNA quality was assessed using RNA 6000 Nano Chips on an Agilent Bioanalyzer (Agilent Technologies) to confirm an RNA integrity score of >7.0. mRNA-seq was performed by Macrogen (Korea) using the Illumina Hi-Seq 2000 platform. RNA-seq libraries were prepared from > 1 µg of total RNA using TruSeq RNA sample prep kit (Illumina) according to the manufacturers' instructions.