Mac’s Feb Goals
February is all about sequencing (and bioinformatics). There are two main sequencing efforts going on this month to assess the DNA methylation status of C. gigas genes. The first is a targeted approach using bisulfite PCR where I have been targeting genes for methylation analysis based either on function (vitellogenin and estrogen receptor) or to confirm results obtained using Nanostring technology (hexokinase). Now, the lab work is done and I am anxiously awaiting the sequencing data. Analyzing these results will help direct future research questions regarding the role of epigenetics in endocrine disruption in shellfish and also determine which samples will be most informative for completing the assays for the Nanostring project this month. The second, a high-throughput bisulfite sequencing effort, resulted in ~140 million 36bp reads. Needless to say, a huge goal for February is to figure out how to best analyze and visualize this data. I am looking at various software applications and ways to visualize the output so that I can understand the results in a biologically meaningful way. Thank goodness there is a support group for problems like this (FSH 546) because it’s pretty darn intimidating. Finally, I’ll be using all that extra February time (you know, with the leap year and all) to try to wrap up a C. virginica manuscript for pub-a-thon II.
