Mac’s Nov Goals
I can’t believe it’s November and I still haven’t published that article on C.gigas DMNT1 yet! Ok, maybe that’s a little unrealistic – and maybe I should just rejoice in the fact that I had a band in my 5’RACE PCR. I’m excited to get the bands sent out for sequencing this week and with any luck (fingers crossed), have 900bp of new DNMT1 sequence to look at. This would make completing some of October’s goals (i.e. gene expression and phylogenetic analysis) a bunch easier.
I don’t want to jinx myself, but I think I can safely say that I have completed the EPA-STAR fellowship application (although I won’t submit until Friday so I’ll continue to obsess about it til then). It will be nice to move on from this and get into the lab to work on making methylation-enriched fractions of fragmented C.gigas DNA using the MethylMiner kit. This ‘4 hour procedure’ has the largest manual I’ve ever seen – but bring it on, anything to get me away from this desk. Once the ‘highly methylated’, ‘less methylated’, and ‘unmethylated’ pools are made they’ll be ready for SOLiD library prep.
Progress was made this month with the Nanostring project to detect site-specific methylation in oysters using the nCounter platform. Codesets have been designed for 56 potentially methylated (CCGG) sites, so in Nov. I’ll be working on getting oyster samples digested with the methylation sensitive restriction enzyme MspI. It will be important to have these digests run all the way to completion, so I’d like to try a few protocols (e.g. serial addition of enzyme, 2 sequential digests, extended single digest) to make sure I’m using the best one.
And, towards the end of the month, I would really like to focus on eating as many carbohydrates (sorry Steven) and as much turkey (and Emma) as humanly possible.
