See notes in post

qPCR

So… I was really hung up on things I’ve read online about how it’s bad if efficiency from a qPCR plate is above 110%… See this GitHub Issue #2487. Chatted with Steven today and he said it isn’t an issue.

So… this week I’m going to go back through all my qPCR plate data files and re-calculate the coefficient of variance for each sample (based on the technical replicates –> ideally the triplicates run (2ul of sample per triplicate) of each sample will not vary much from each other) and I’ll also check the Cq of the standard curves for each plate and plot them real quick in excel or google sheets or something as a sanity check.

I’ll prepare some slides and notes on how I’m doing all the calculations and things to share with Steven and Sam sometime this week to get their feedback.

DNA extractions

I’ll continue on with those for sure this week so that all the DNA is ready to be run on plates in the meantime. I have 32 mussel tissue samples to run (so that’ll be two DNA extraction batches – each one 16 samples + 2 DNA extraction blanks to keep the centrifuge balanced). I have 40 (that’ll be two DNA extraction batches – each one 20 samples + 2 DNA extraction blanks to keep the centrifuge balanced).

I tested out 4 different tissue weights with 2025 mussels that weren’t part of last year’s experiment but were just kind of thrown in as an aside – see post: here. Essentially, DNA was in all samples, with the most in M4B, which was 15mg of whole body homogenized tissue.