G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [RNA-seq]

G-quadruplexes are secondary DNA structures which have been shown to have an impact on gene transcription via a variety of mechanisms, In this study we generate RNA-seq data of wildtype chemotherpay sensitive (PEO1 A) and chemostherapy resistant (PEO4 A) ovarian cancer cells to intersect with G-quadruplex mapping data to assess how transcription is impacted by G-quadruplex formation. In another variation of the PEO1/4 cell line, in which the PEO1 B cell line has a reversion mutation to reinstate BRCA2, we used the G-quadruplex stabilising molecule pyridostatin (PDS) to treat PEO1 B and its counterpart PEO4 B for either 0, 2 or 6 hours to see how stabilising G-quadruplexes effects gene expression in a temporal manner. We performed RNA-seq on wildtype PEO1 (BRCA2-) and PEO4 (BRCA2+) cells (which we term PEO1 A and PEO4 A) to assess differential expression between the two. We then performed RNA-seq on another variation of the PEO pair in which BRAC2 has been reinstated in PEO1, before and after treatment with PDS for 2 and 6 hours. We term this pair with the altered BRCA2 status PEO1 B and PEO4 B. 3x biological replicates were performed for each sample type.