Additional file 11: Figure S6.

(a) Venn diagram showing the overlap between upstream divergent RNAs (udRNAs) and antisense transcription start site (TSS)-associated (TSSa) RNAs at the TSS. (b) Venn diagram showing that 44.69% (274 of 613) udRNAs overlapping with divergent long non-coding RNAs (lncRNAs) were also upregulated after 7SK knockdown. (c) Venn diagram showing the overlap between genes with failed termination after 7SK knockdown (‘hotspot’ genes) and 7SK-regulated udRNAs. (d) Quantitative reverse transcription (qRT)-PCR analysis of Hexim1 total RNA, and Dll1 nascent RNA, 6 hours after nucleofection of embryonic stem cell (ESCs) with scrambled 7SK 3′ antisense oligonucleotides (ASOs) targeting the 3′ segments of 7SK, in the presence or absence of I-BET151. Error bars represent standard error of the mean (SEM) from two to three independent experiments. (e) Box plot depicting log2 fold changes measured by RNA sequencing (RNA-seq) after 7SK knockdown of udRNAs and their associated genes in mouse ESCs, using either 7SK 5′ or 7SK 3′ ASO data for udRNA detection.

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Castelo-Branco et al. Genome Biology 2013 14:R98   doi:10.1186/gb-2013-14-9-r98