RNA-Seq of human breast cancer cells to identify differential miRNA regulation due to RNA editing

We conducted RNA-Seq on two human breast cancer cell lines (MCF-7 & MDA-MB-231) to identify RNA editing events mediated by the adenosine deaminase protein ADAR and to investigate how these sequence alterations affect miRNA regulation. Two RNA-Seq protocols were conducted: 1) a polyA selected experiment to isolate mRNA for edit identification, and 2) a size selected experiment where small RNAs ranging from 17 to 35nts were sequenced to identify miRNAs that were differentially expressed between the two cell lines. Raw paired-end reads were received totaling around 6 billion base pairs per cell line.