RNA-seq Analysis of Transcriptome Changes

RNA whole transcriptome sequencing (RNA-seq) was carried out at 0 (1 replicate), 4 (2 replicates), 12 (1 replicate) and 36hrs (2 replicates) post tamoxifen treatment on polyA selected RNA using Illumina tru-seq library construction. RNA-seq was also carried out for the over-expression experiments in parental MCF10A cells that were untransduced (3 replicates), transduced with LINC00520 (2 replicates) or transduced with a control lincRNA AC006262.6 (2 replicates) on polyA selected RNA using Illumina tru-seq library construction harvested 72 hours post transduction.
Transcript levels were quantified and differentially expressed genes were called using cuffdiff2 [40 (link)]. Relative transcript levels are expressed as a “Fragments Per Kilobase of transcript per Million mapped” (FPKM) which corrects for the length of the transcript and the depth of the libraries. Raw and processed ChIP-Seq data was retrieved from [18 (link)].