Differential methylation analysis of low pH vs ambient conditioned geoduck hemolymph

  • methylkit on Emu errored out because the treatment variable was in list format and needs to be a vector. So I am rerunning it via the Emu Rstudio web interface on Ostrich
  • methylpy DMRfind completed and the output it here:
    • Since the output is all DM sites and not DMRs, I need to figure out how to get DMRs. I’m not sure why the package didn’t automatically do this. I am following the nature paper’s pipeline and found the additional analysis scripts they used. But I need to figure out how to apply them to this output.

oyster proteomics

Still trying to wrap my head around this paper and come up with a straight-forward story. Here are some thoughts:

How does temperature alter physiology to make cultures less likely to crash?

  • temperature speeds up development:
    • this has been previosly observed
    • 29C proteomes seem to correspond with 23C proteomes that are from subsequent timepoint, based on the PCA
    • animals are larger at 29C
  • We have proteomes to know that oysters are on track for “normal (23C)” and “accelerated (29C)” development

  • are there differences beyond a shift in development time/size?