January Goals recap

West Coast Green Crab Experiment:

• I’m still at decontamination station…but there’s been some progress in understanding WHY I’m there.
• Trained Vanessa in PCR and gel analyses

Coral Transcriptomics:

• Addressed Ann’s comments on the methods and results

Green Crab Pilot Experiment:

• Updated methods and results from metabolomics and lipidomics analyses
• Started reviewing green crab thermal physiology literature

Hawaii Gigas Methylation:

• Sigh. Another month not actually getting to any of this.

Other:

• Submitted three additional faculty applications
• Worked on PRISMA searches for WOCinEEB Global Change collaboration
• Monitored RIE2 email and updated database

February Goals

West Coast Green Crab Experiment:

• Figure out contamination issues
• Complete extractions and PCR for TTR crabs
• Conduct preliminary individual-level analyses

Green Crab Pilot Experiment:

• Continue reading green crab thermal physiology literature
• Revise metabolomics analysis
• Revise lipidomics analysis
• Update methods and results

Coral Transcriptomics:

• Modify analytical methods based on feedback
• Update methods and results
• Update supplementary material
• Write discussion
• Write abstract

Hawaii Gigas Methylation:

• Finish methylKit contingency tests
• Conduct a randomization test for DML identification
• Integrate other epigenetic datasets
• Update methods and results
• Revise discussion

Other:

• Seminar at URI
• Submit additional faculty applications
• Review NSF proposal
• Launch RIE2 survey
• PRISMA searches for WOCinEEB Global Change collaboration
• Extract metadata for the WOCinEEB Global Change collaboration

Deep Freeze

Things that are not immediate enough to be on the backburner, so they’re stuck in the deep freeze.

Virginica Methylation and Expression:

I’ll return to this when I have an updated discussion for the Hawaii paper.

• Update methods and results from quadratic addition to transcriptional noise model
• Compare transcriptional noise analysis with Liew and Aranda papers

Killifish Methylation and Expression:

I’ll return to this when I have a good draft of the coral paper.

• Pathway analysis for RNA-Seq data
• Determine protocol for SNP identification
• Conduct in silico RRBS digestion
• Characterize DEG that overlap between populations
• Quantify gene expression variability
• Visualize DEG data

Zebrafish DNMT:

I’ll think about this once I have a robust killifish paper draft.

• Identify a stress condition to use for the zebrafish based on disease factors or conditions that are known to induce changes in methylation
• Determine physiological endpoints to assess for embryos
• Construct a project timeline