N6-methyladenosine (m6A) profiling of ovarian cancer tissues

We developed RADAR , a method for detecting differential methylated loci in MeRIP-seq data. RADAR uses a flexible model to accommodate increased noise due to RNA immunoprecipitation and are compatible with complex study design. RADAR enabled accurate identification of altered methylation sites in patient samples where covariates need to be accounted for. We use the m6A-profiling of ovarian cancer data as an example data set to benchmart the performance of RADAR and a few alternative methods. Overall design: Six omental tumor tissues were collected from newly diagnosed patients with advanced, metastatic high-grade serous ovarian cancer. Seven normal fallopian tube tissues were collected from patients with benign gynecological conditions. Total RNA was extracted from the tissue by TRIzol followed by fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Takara Pico-Input Strand-Specific Total RNA-seq for Illumina was used to construct library from total RNA where ribosome-derived cDNA was removed before final library amplification. The libraries were sequenced by the NextSeq 500 platform at PE37 mode.