Hi. It’s been a while since I wrote some concrete goals! But seeing how this is my last month on my WHOI Postdoctoral Scholarship before I transition to the NSF PRFB, I thought it would be good to assess the status of my current projects and do some prioritizing.

December Goals + the first bit of 2023 recap

Coral Transcriptomics:

• Solidified OrthoFinder methods
• Got results from the OrthoFinder analysis!
• Worked on HRE analysis
• Updated methods and results in paper

Green Crab Pilot Experiment:

• Continued working with Sara on demographic data analysis
• Paused this to devote my full attention to the coral project

Hawaii Gigas Methylation:

• Restructured paper to reflect a move back to methylKit
• Sam extracted SNPs with EpiDiverse, but I haven’t looked at the output

Virginica Methylation and Expression:

• Revisited transcriptional noise analysis

Other:

• Launched the postdoc mentoring program!
• I haven’t distributed the postdoc mentoring survey results, but I’ll have the next set of PDA representatives do that
• Started applying mindful productivity tenets to my working habits

March Goals

My main focus for March is to get the coral project in a place where I can shift to writing. This means having all analyses completed, methods and results written, and an outlined discussion. My goals reflect this priority!

Coral Transcritomics:

• Finish remaining analyses
• Update methods
• Update results
• Outline discussion
• Get Ann or Maggie to provide comments on materials written

Hawaii Gigas Methylation:

• Add Rajan’s edits as comments to the draft manuscript
• Review EpiDiverse output and create a new SNP list
• Rerun methylKit
• Conduct a randomization test for DML identification
• Update methods and results

Green Crab Pilot Experiment:

• Determine workflow for metabolomics sample processing
• Order materials for metabolomics samples
• Finish demographic data analysis
• Update methods and results

Virginica Methylation and Expression:

• Update results with initial mixOmics analysis
• Revise gene-based transcriptional noise model
• Create sample-based transcriptional noise model
• Look into spurious transcription methods
• Create a SNP list from EpiDiverse output

Other:

• NSF PRFB start paperwork
• Eelgrass transcriptomics reviewer comments
• Module 1 of mindful productivity for scientists class

Deep Freeze

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

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