RNA-seq analysis of control and NRDE2-depleted breast cancer cells

Purpose: investigate transcriptomic changes following depletion of the NRDE2 gene Methods: MDA-MB-231 breast cancer cells were transfected with 20nM control or NRDE2-targeting siRNAs, and RNA was collected after 48h for RNA-seq analysis Results: We analyzed si-Control and si-NRDE2-treated samples in triplicate (~46-64 million reads per sample) and find that the near-complete loss of NRDE2 results in generally modest changes in gene expression, with only 84 genes deregulated >2-fold. We also identify 342 introns which are differentially retained in NRDE2-depleted cells. Conclusions: NRDE2 is required for suppressing intron retention in a subset of genes mRNA profiles of control and si-NRDE2-treated MDA-MB-231 cells were generated in triplicate by RNA-seq, using the Illumina NextSeq500 platform