Supplementary Figure 4: Pausing-index changes in replicates.
From: TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release
(a) Scatter plots depict per-replicate TRIMKD vs. WT pausing index fold change on log2 scale, as a function of WT pausing index (N= 8,652 (Rep #1), 8655 (Rep#2)). Plots do not include genes with undefined pausing index resulting from zero promoter or gene body read density in either condition. (b) Zoom-In views of plots shown in a, between 0 and 300 in pausing index in WT. (c) Scatter plots of raw pausing indices of replicate 1 versus replicate 2 for WT and TRIM28 KD. Plots were generated combining the genes with RPKM greater than 1, for all samples in both the promoter and gene body window (N=601). (d) Summary of paused genes regulated by TRIM28. Paused genes are defined using the following criteria: gene body and promoter windows >=50% mappable and p-value <= 0.001 (poisson probability of observing X or greater promoter density given expected value equal to gene body density). Paused genes have pausing index equal or greater than 5.
