Supplementary Figure 2: GRO-seq controls.
From: Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis
(a) Meta-analysis of GRO-seq signals across all RefSeq genes >1kb in A549 cells upon infection with influenza PR8ΔNS1, before (dashed lines) and 4 hours after infection (solid lines) in siCtrl (blue) and siSETX (red) treated cells. Y axis indicates the geometric mean coverage per 5 million reads. (b) Travelling ratios (TR) of all active genes for the conditions indicated in (a). TRs were calculated as the average number of tags per bp in the promoter-proximal region (30 to +300 bp around TSS) divided by that on the gene body (+300 bp to the end of the gene). The number of active genes identified in each condition is indicated between brackets. (c) GRO-seq read coverage for the RPL10 gene, showing no changes in siCtrl over siSETX conditions. Y-axis indicates base coverage per 5 million reads. (d) Overview of the fraction of GRO-seq reads mapping to genic (exons, introns and antisense) and intergenic regions. (e) Expression of IFNB1 and IFIT1 mRNA levels in siSETX and siCtrl A549 cells in the presence of flavopiridol (blue bars), DMSO vehicle control (red bars), or untreated control cells (gray bars). Values represent the mean and standard deviation of three independent experiments; Asterisks (*and **) indicate t-test p-values < 0.05 and < 0.005, respectively.
