So turns out it’s April and I feel like Daniel Radcliffe.

March Goals Recap

Gigas Gonad Methylation:

• Submitted the manuscript! Had a few back-and-forth QC requests but last I checked reviewers have been contacted. A version is available on bioRXiv.

Coral Transcriptomics:

• Extracted a batch of test samples and sent them for preliminary sequencing

Killifish Methylation and Expression:

• Tested mapping code on a subset of samples
• Determined that mapping should be done non-directionally
• The corrupted sample couldn’t be fixed, so I proceeded with the full sample mapping without that sample!

Virginica Methylation and Expression:

• Worked on mixOmics SPLS and finished the analysis for all samples
• Started sex-specific SPLS, but kept running into a specific code issue
• Didn’t get a chance to update any of the methods and results

Other:

• Still working on that ocean acidification and reproduction review…
• Submitted eelgrass transcriptomics abstract, and it was accepted immediately!
• Discussed zebrafish project logistics with Neel
• Coordinated the pre-application postdoctoral mentoring program
• Didn’t apply to any positions because I found out I got the NSF PRFB!

April Goals

Coral Transcriptomics:

• Evaluate next steps for the project

Killifish Methylation and Expression

• Finish full sample mapping
• Extract methylation and filter methylation calls
• Determine how to conduct analysis of DMR with multiple factors (population and hypoxia)

Zebrafish DNMT:

• 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

Virginica Methylation and Expression:

• Update methods
• Update foundational results
• Continue working through sex-specific SPLS

Other:

• Think about potential components for silverside project
• Send out postdoctoral mentorship survey
• Coordinate pre-application postdoctoral mentoring program
• Apply to any relevant faculty positions or funding opportunities

Deep Freeze

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

Hawaii Gigas Methylation:

Once the reproduction review and eelgrass paper are in a stable state, I can start thinking about this paper again.

• Address Rajan’s edits
• Review DSS script and determine if I should go back to methylKit for better interpretation
• Extract SNPs with EpiDiverse and create a relatedness matrix
• Look at methylation islands and non-methylated regions
• Examine overlaps between DML and other epigenomic datasets from Sascha