Fig. 3

Changes in the abundance of intronic regions with HIV infection. Expression of intronic and exonic regions was quantified as the proportion of reads mapping within the intron/exon out of the total reads mapping to the transcription units overlapping that intron/exon. a Comparison of the ratios of expression between infected and uninfected replicates in exclusively intronic or exonic regions of transcription units. b Reproducibility of intron retention between replicates. Each point quantifies the change in expression with HIV infection for a specific intronic region. The x-axis shows changes in gene activity accompanying infection for one set of replicates (Infected-1 and Infected-2 vs. Uninfected-1) and the y-axis shows the same data for different replicates (Infected-3 vs. Uninfected-2). c Reproducibility of intron retention between studies. The plot is arranged as in b but with all data from our study combined on the x-axis and corresponding data from Chang et al. [25] on the y-axis