Alberto Riva assisted the McKnight Brain Institute in a big methylation study over the past year. The study was published in the Frontiers in Aging Neuroscience journal.
The purpose was to determine whether there is a relationship between the decline of cognitive function with aging and epigenetic changes in neurons. The study was performed on rats using a combination of whole-genome bisulfite sequencing (WGBS) to analyze methylation changes, and RNA-seq to investigate downstream effects on gene regulation.
One important feature of this study is the relatively large number of animals involved (10 young rats and 20 aged), which is uncommon for this kind of project. This required a computational pipeline for methylation analysis in order to handle a such large number of samples, which was Riva’s role in the project. They relied on HiPerGator for raw computational power. Riva wrote a new methylation analysis tool, CSCALL, specifically designed to handle multiple replicates of each condition in an efficient and accurate way. This new pipeline, including CSCALL, is now part of the standard arsenal of analysis services offered by our core.
The WGBS was also performed by ICBR’s Next Gen Sequencing Core.
Read Study: http://journal.frontiersin.org/article/10.3389/fnagi.2017.00249/full#h11