lincRNA primers were designed using primer3 (http://frodo.wi.mit.edu/primer3/). Specifically, we designed primers spanning exon-exon junctions by specifying each of the regions as preferred inclusion regions in the primer3 program. When a low scoring primer pair (primer penalty <1) was available it was used. If none was available, we then identified all primers that contained amplicons that spanned an exon-exon junction. In a few cases, when we could not identify a primer pair spanning an exon-exon junction, we designed primers within an exon of the lincRNA. For each primer pair, we tested the specificity against the transcriptome57 (Ref Seq NCBI Release 39) and the genome (Mouse MM9) using the isPCR (http://genome.ucsc.edu/cgi-bin/hgPcr) program. Specifically, we required that the primer pair amplify the lincRNA gene and no other genomic of gene amplicon.
