title: Over-expression of DNA methyltransferase MET1 in Arabidopsis generates new epi-alleles with heritable expression states
design: Next generation sequencing libraries were created from mRNA using the TruSeq Stranded mRNA kit (Illumina) and sequenced on a HiSeq 2500 to generate 50 bp single end sequence data. The data was aligned to the Arabidopsis genome (TAIR web site [https://www.arabidopsis.org]) using the STAR aligner (Dobin et al., 2013). Reads mapping to each transcript were determined and pairwise comparisons between the wild type sample and each of the modified samples were performed using CuffDiff (Trapnell et al., 2013) and used to identify transcripts whose expression varied markedly between the control and experimental sample for each condition