Small RNA sequencing of MCF10A cells after doxorubicin treatment
Total RNA was purified using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. Small RNA libraries were created using the TruSeq Small RNA preparation kit (Illumina, RS-200-0012) with variable index primers to allow for multiplexing of samples. The protocol provided by the manufacturer was used to create libraries using 0.5 µg total RNA. Three biological repeats were done for the doxorubicin treatment of cells. Libraries were sent to The Genome Analysis Centre (TGAC), Norwich, where they were checked on a BioAnalyser (Agilent DNA 2100 chip) and LabChip GX, followed by quantification. Libraries were then pooled and sequencing on Illumina HiSeq 2500 (Rapid-Run mode, cBot clustering) platform using 50 bp single end reads.