Final push for the year! I made some good progress on postdoc and side projects last month, and want to continue working on postdoc projects in particular so I can have a manuscript submitted in a month or so. I (once again) have lofty goals for this month because I have too many things that feel high priority right now! Perhaps next year (yikes) I can reassess.

November Goals Recap

Coral Transcriptomics:

• Ran WGCNA and GO-MWU analyses!
• Updated methods and results
• Determined next steps for project

Killifish Methylation and Expression:

• Decided not to continue with the new genome for now, since the sample used is from Georgia and killifish populations have high genome variability. The old genome uses a sample from Maine which is likely more similar to the samples we have.
• Started pathway analysis but could not move forward because of missing information
• Reviewed existing lab data with Mark!

Green Crab Pilot Experiment:

• Met with Chris to learn about respiration data analysis
• Worked with Sara to analyze baseline demographic data by treatment and time!

Other:

• Reviewed supplementary material for eelgrass transcriptomics paper
• Finished applying for faculty positions

December Goals

Coral Transcriptomics:

• Test OrthoFinder methods
• Obtain lists of orthologous DEG from other studies
• Update methods and results

Killifish Methylation and Expression:

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

Green Crab Pilot Experiment:

• Continue working with Sara on demographic data analysis
• Analyze survivorship data by treatment and sex
• Analyze time-to-right data by treatment, sex, weight, and integument color
• Update methods and results
• Determine workflow for metabolomics sample processing
• Order materials for metabolomics samples

Hawaii Gigas Methylation:

• Address Rajan’s edits
• Return to methylKit for better interpretation
• Conduct a randomization test for DML identification
• Extract SNPs with EpiDiverse and create a relatedness matrix
• Examine overlaps between DML and other epigenomic datasets from Sascha
• Determine a method for assessing methylation variation by copy number
• Update methods and results
• Update discussion
• Get paper ready for submission!

Other:

• Launch postdoc mentoring program
• Distribute postdoc mentoring survey results

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 will revisit this paper after I finish the Hawaii paper.

• Revisit transcriptional noise analysis
• Try and recreate model from Aranda paper

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