Shelly’s Notebook: Mon. April 8, 2019 Salmon Sea lice Project

Salmon sea lice project

  • met with Steven and Christian today about directions for epigenetic exploration of salmon infected with sea lice
  • need to determine best method for epigenetic analysis for these samples (e.g. ATAC-seq, amplicon BS-seq, ChIP-seq, etc.)
    • it’s hard to say how well the chromatin structure is maintained in ethanol fixed samples (see ATAC-seq references on Epigenome methods slide. This could contribute to variation between individuals.
    • From the references I found so far (see Epigenome methods slide), it seems like RRBS or amplicon BS sequencing would be the better way to go.

from shellytrigg

Grace’s Notebook: Bairdi RNA extractions- other methods to try; Plan for Week

Between trying to add some edits and clean things up for the 2015 Oysterseed project paper, I’ve been reading protocols for other RNA extraction kits. Zymo Quick-DNA/RNA Mircoprep Plus Kit, Zymo Directzol RNA MiniPrep… Details in post

Zymo Research Quick-DNA/RNA Microprep Plus Kit

Cat. D7005
Manual pdf

This was recommended to Sam and I from Pam. Sam requested a free sample, which should be arriving some time this week.

Zymo Direct-zol RNA MiniPrep

Cat. R2050
Manual pdf

We already have this from when Hollie was here in 2016. There’s one box that’s opened, and one unopened 50rxns kit box.

This week


I’ll be able to try out both kits (Microprep should arrive this week; we already have Direct-zol)


Intro: update it and tailor it more to the project
Methods: get them in a solid state – address all comments and get details right
Results: identify all results and include in paper; are we using phenotypic data even though I can’t get it for just the control silos?
Discussion: write it up after results are finalized

Skyline document: finish publishing it to Panorama (need project title, abstract in order to finalize publication)
Have this all done by next Wednesday
I think once the results are finalized, I’ll feel able to finish up Intro and Discussion

from Grace’s Lab Notebook