This past month was spent juggling analyses and experimental set-ups: an endless conveyor belt of work. But I’d like to think I was more successful than Lucy and Ethel because I feel good about the progress I made!

May Goals Recap

Killifish Methylation and Expression

• Troubleshooted my BAT_overview and BAT_DMRcalling issues!
• Identified DMR and revised DMR identification without L4 samples
• Characterized the general methylation landscape
• Update methods and results for methylation dataset
• Didn’t start RNA-Seq analysis since Neel and I decided that I could use the analysis he already did for preliminary results, and I could redo both the RNA-Seq and RRBS analyses with the new genome later

Green Crab Pilot Experiment:

• Got space in ESL for my experiment!
• After much struggle, determined that the cold box could hold temperature at 5ºC ± 2ºC
• Slowly started putting together the experimental tanks, air lines, and heaters
• Worked with Chris to find a time to learn respirometry
• Reworked the experimental timeline and decided on a tentative start timeframe

Virginica Methylation and Expression:

• Updated foundational methylation dataset methods and results
• Didn’t return to SPLS and worked on transcriptional noise analysis with Shelly

Coral Transcriptomics:

• Came up with a project plan with Maggie!

Other:

• Got SO CLOSE to submitting the reproduction review
• Finished my work with the eelgrass paper
• Extended the mentorship experiences survey deadline to get additional responses

June Goals

Killifish Methylation and Expression:

• Finalize DMR identification and annotation
• Integrate RRBS and RNA-Seq analysis
• Start RRBS mapping with new genome
• Update methods and results

Green Crab Pilot Experiment:

• Finish experimental set up
• Complete respiration trial and obtain any necessary materials
• Finalize experiment start date
• Obtain crabs and crab food

Virginica Methylation and Expression:

• Finish transcriptional noise analysis
• Return to SPLS
• Determine which hypothesis-driven analyses from the workshop should be incorporated into the paper or redone

Other:

• Submit reproduction review paper
• Distribute results of postdoctoral 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.

Coral Transcriptomics:

Once I finish my preliminary killifish analysis, I will work on this.

• Conduct preliminary Tag-Seq differential expression analysis

Hawaii Gigas Methylation:

Once the reproduction review and eelgrass paper are submitted, I can start thinking about this paper again.

• Address Rajan’s edits
• Return 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