Spent a lot of time in April coding! Which means I was the bottom-right Nick Cage on more than one occasion.

April Goals Recap

Coral Transcriptomics:

• We decided to evaluate some existing datasets and think about extractions for a different experiment later

Killifish Methylation and Expression

• Finished mapping all samples, extracting and filtering methylation!
• Started testing the analysis module but ran into a few issues

Green Crab Pilot Experiment:

• Spoke to Carolyn and we decided to get a pilot experiment going for this summer!
• Drafted an experiment plan
• Got in contact with Rick to determine which facilities to use for this experiment
• Found tanks, heaters, and chillers that could be used
• Spoke with Zac and Chris about respiration methods

Virginica Methylation and Expression:

• Ran into a computational issue for SPLS tuning, so I paused
• Updated foundational methods and results

Other:

• Sent out postdoctoral mentorship survey! I also contacted the chairs of departmental mentorship committees to get them to circulate it.
• Got the go-ahead for the pre-application postdoctoral mentoring program!
• Kept my eye out for any relevant faculty positions or funding opportunities

May Goals

Coral Transcriptomics:

• Evaluate the existing dataset and discuss plans with Maggie

Killifish Methylation and Expression

• Characterize the general methylation landscape
• Identify and annotate DMR
• Update methods and results for methylation dataset
• Start RNA-Seq analysis

Green Crab Pilot Experiment:

• Identify a facility I can use for experiments
• Determine the coldest temperature that I can achieve
• Practice respirometry methods with crabs
• Plan for the start date!

Virginica Methylation and Expression:

• Finish updating foundational methylation dataset methods and results
• Return to SPLS
• Determine which hypothesis-driven analyses from the workshop should be incorporated into the paper or redone

Other:

• SUBMIT THE REPRODUCTION REVIEW
• Continue working on the eelgrass paper
• Disseminate the results of the mentorship experiences survey
• Launch the postdoctoral mentoring program
• Apply for 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 submitted, 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

Zebrafish DNMT:

I’ll think about this once I finish my pilot experiment.

• 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