<p>Total RNA from the different pooled sucrose gradient fractions were extracted and prepared for Affymetrix analysis. The input sample is the non-fractionated total RNA sample. The data for vegetative samples were ‘.cell’ files from Dominissini et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132090#pone.0132090.ref006" target="_blank">6</a>] The raw chip data were analysed using Partek GS 6.0 software package. The gene list of significant genes (FDR<0.05, no fold change cut off was applied) was the base for hierarchic clustering using Partek GS 6.0. 12 different clusters were identified (labelled by different colour bars) (a). The gene lists for each different cluster were used to determine the enrichment for methylated transcripts using the yeast methylome from Schwartz <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132090#pone.0132090.ref017" target="_blank">17</a>]. The statistical significance of the overlaps was determined using the online resource <a href="http://nemates.org/MA/progs/overlap_stats.html" target="_blank">http://nemates.org/MA/progs/overlap_stats.html</a> (b).</p
