Posted on December 11, 2018
Right now, seven Early Stage Researchers (ESRs) from the Marie Skłodowska-Curie Innovative Training Network EpiDiverse, majoring in biology, are trained by our ESR Adam in using the earlier developed WGBS and DMR calling pipelines. With three ESRs hosted by Prof. Dr. Peter F. Stadler at the bioinformatics chair of Leipzig university and four ESRs at ecSeq Bioinformatics, they are located in walking distance from each other. Thus, all of them have the unique possibility to get trained by experts from academia and industry. Two different views, two different working methods, one goal.
They already analyzed the first 24 bisulfite-treated DNA-Seq samples from pennycress (thlaspi). With 20GB per sample, our high-performances computer clusters ('epi' and 'diverse') were under heavy load. It took 20 hours to map the 24 samples to the thlaspi genome using the tool erne-bs5, while the other tool, segemehl, needed around one week. Calling differentially methylated regions (DMRs) with the tool metilene took ~4h.
Now the ESRs are trained by experts within the EpiDiverse network in how to interprete the results. By overlapping the DMRs with annotations, important meta information such as their genomic position (intron, exon, promoter) is added to the significant regions. Filters, clustering methods and elaborate visualizations will help the researchers to carve out relevant regions that are differentially methylated in stress situations and/or between different environmental conditions.