Methylation Nomenclature

A reviewer recently pointed out we had not used standard descriptions for the methylation data we were reporting. At first I didn't think this was necessary but looking at the paper they refer to I think it is a good idea to try to keep to a standard. Link to paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523709/pdf/nihms426104.pdf

Confirmation of Differential or Allele-Specific Methylation

Here is a brief pipeline for confirming allele specific methylation (or differential meth with some modifications) in known genes (like qPCR for gene expression). The above protocol was specifically for confirming methylation in different alleles. However this could be adapted to confirm methylation levels in known genes between different samples. Also the TOPO closing says … Continue reading Confirmation of Differential or Allele-Specific Methylation →

Permute? or no?

This post covers brief findings from exploring permutation tests when looking for differentially methylated genes from whole genome bisulfite sequencing. The idea behind it: if we randomly shuffle the data between control and treatment samples and see roughly the same number of genes coming out as differentially methylated then we can't say the genes we originally … Continue reading Permute? or no? →