Extended Data Fig. 3: Percentage of unproductively spliced reads upon knockdown of NMD factors.
From: Global impact of unproductive splicing on human gene expression
(a) Fraction of splice junction reads in each short read steady-state RNA-seq sample that are in Gencode-annotated productive transcript structures (blue), versus unannotated or annotated unproductive transcript structures (gray). Biological replicates represented by each column, with dashed lines to indicate median for each group. NMD factors were knocked-down (KD) singly or as double knockdown (dKD) with shRNA in HeLa cells with an shRNA scramble control24. (b) Nanopore long-read sequencing quantifies the percent of full-length reads that are targeted by NMD, defined as containing at least one unproductive junction, as a function of the number of splice junctions in the read. Knockdown experiments of similar design as in (a)23.
