February was a short month (even with the extra day where nothing was impossible #30Rock) but I managed to do a lot! Am I finally getting the hang of things? Maybe…but I am going on vacation at the end of this month so things are bound to fall apart.

February Goals recap

West Coast Green Crab Experiment:

• FIGURED OUT MY CONTAMINATION ISSUES! Turns out it was an issue with primer stock AND samples
• Chugging along on my extractions. Vanessa and I have finished most of the sampled TTR crabs.
• Conducted preliminary individual-level analyses

Green Crab Pilot Experiment:

• Started reading green crab thermal physiology literature
• Presented revised metabolomics analysis and future ideas in lab meeting
• Updated the GLM methods for respirometry analysis

Coral Transcriptomics:

• Modified analytical methods based on feedback
• Updated methods and results
• Updated supplementary material
• Wrote my portion of the abstract

Virginica Methylation and Expression:

We’re gearing for a March submission of the CEABiGR paper, so I moved this out of the deep freeze.

• Updated methods and results from quadratic addition to transcriptional noise model
• Modeled the shift in the predominant isoform
• Summarized gene activity information
• Visualized predominant isoform analysis results
• Conducted an enrichment test for the genes where the predominant isoform shifted

Other:

• Gave a seminar at URI fully about my crab data!
• Continued PRISMA searches for WOCinEEB Global Change collaboration

March Goals

Virginica Methylation and Expression:

• Address all analyses in [this issue]
• Create all figures in [this issue]
• Compare transcriptional noise analysis with Liew and Aranda papers in discussion
• Write discussion
• Write introduction
• Write abstract
• Send manuscript to co-authors
• Incorporate co-author feedback
• Submit manuscript

West Coast Green Crab Experiment:

• Finish extractions, PCR, and gel for all remaining crab samples
• Send samples for sequencing

Green Crab Pilot Experiment:

• Continue reading green crab thermal physiology literature

Coral Transcriptomics:

This will depend on when Maggie gets back from the field. Since I can’t do a lot independently at the moment, these may or may not get done this month.

• Finalize abstract
• Outline discussion

Other:

• Sort duplicates for WOCinEEB Global Change collaboration
• Send papers to the appropriate groups
• Supervise Sophia’s data extraction
• Take care of RIE2 tasks

Deep Freeze

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

Hawaii Gigas Methylation:

I’ll return to this next month, after we submit the CEABiGR paper this month.

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

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