Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells

The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LCC9 tamoxifen-resistant breast cancer cell lines relative to parental MCF-7 tamoxifen-sensitive cells Overall design: Methods: MCF-7 and LCC9 cells were transfected, in three separate experiments, with pre-miR-29b-1, pre-miR-29a, or anti-miR-29a (which blocks both miR-29b-1 and miR-29a). RNA seq profiles were generated by deep sequencing, in triplicate, using Illumina Nextseq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.