Yesterday, I described how I planned to start with a comparison of Day 0 and Day 17 libraries at ambient temperatures. I was able to complete that! Methods followed the same protocol outlined previously - use Kallisto to create pseudoalignments for libraries, use a script from Trinity pipeline to create matrix of counts, put matrix of counts into DESeq2 and analyze. Here are links to the following results:

The most important of those is likely the table of genes with significantly different expressions, but before I do much with that, I’m going to do the next 3 comparisons, as follow:

  • Day 0+2 Elevated vs Low (127/173/72/272/280/294 vs 151/254)
  • Day 0+2 Elevated vs Ambient (127/173/72/272/280/294 vs 118/132/178/334/349/359)
  • Day 0+2 Ambient vs Low (118/132/178/334/349/359 vs 151/254)

Hopefully I’ve got enough storage space for all those libraries!