Additional file 1: of Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin

TopHat2/Cufflinks revealed 146,910 transcripts/isoforms with the min-isoform-fraction (-F) set to 0.05 (default setting). 16,532 out of the 146,910 isoforms were known protein-coding genes (class code =). Overlapping transcripts (OT) were identified using Cuffcompare by extracting transcripts with class code x and s from the merged GTF file. Transcripts with class code i, o and u were also extracted and further processed using Bedtools intersect (option -S) to sort antisense OT. In total, there were 14,774 OT fitting these criteria. The 14,774 OT were subjected to PLEK analysis to predict lncRNAs. PLEK revealed 5299 OT lncRNAs. 75% of the OT lncRNAs are unannotated intergenic transcripts with class code u. The remaining 25% are lncRNAs that overlap with an exon of a protein-coding gene. Of note, after PLEK, there were no single exon transcripts. (EPS 1498Â kb