MOESM5 of Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

Additional file 5: Expression observed in the top 50 most differentially expressed introns in ribosomal protein genes and ERV-9/LTR12C regions with expression continuing for greater than 1000bp downstream. A) RNA-Seq read counts for the 50 most differentially expressed in introns in ribosomal protein genes. The number of reads covering each base is shown on the y-axis. UCSC genes and RepeatMasker LTRs are annotated below with lines indicating introns and boxes indicating exons or repeats. Dashed vertical lines highlight the region detected as differentially expressed. B) As in A but showing RNA-Seq read counts for ERV-9/LTR12C with expression continuing for greater than 1000 bp 3′ of the LTR region. LTRs were selected by filtering for regions with a 90th percentile coverage higher than 30 and looking for the furthest 3′ base with continuous (no gap greater than 200 bp) coverage of at least 10 % of the 90th percentile of expression within the LTR.