Comparison of RNA-Seq datasets from mouse embryonic stem cells before and after knockdown of 7SK RNA. (a) UCSC Genome Browser tracks of a representative 6 million bp region showing the original control and 7SK knockdown RNA-Seq datasets from Castelo-Branco et al.. The top two tracks show only the forward direction, with transcription proceeding toward the right. As described in the text, these two tracks were fed into a bioinformatics pipeline that included a subtraction of the control data from the 7SK knockdown data; the difference track is displayed as the third track (KD - control for), and then again as the fourth track (KD - control for), but in this case with an adjustment to cut-off values below −0.01. A difference track with a −0.01 cut-off was also generated from the reverse reads (KD - control rev, bottom track). Arrows indicate regions of runaway transcription. All tracks in the figure, together with other related datasets, have been deposited in the Gene Expression Omnibus (GSE50860). (b) UCSC Genome Browser tracks of a multi-gene region, including a gene encoding a ribosomal protein. The top two tracks display the original data for control and 7SK knockdown cells (Control for and 7SK KD for, respectively). The bottom row displays the difference track with a −0.01 cut-off. (c) Same display as for (b), but for the multi-gene region surrounding a different ribosomal protein gene. Only the difference track is shown.