July Goals Recap

Green Crab Pilot Experiment:

• Finalized respirometry and time-to-right protocols
• Completed an experiment!

Coral Transcriptomics:

• Wasn’t able to finish the TagSeq analysis but I started to gather the components I needed for the bioinformatic analysis

Killifish Methylation and Expression:

• Wasn’t able to make much progress on this project because of the experiment

Virginica Methylation and Expression:

• Finalized methylation data and results

August Goals

Coral Transcriptomics:

• Complete initial TagSeq analysis and discuss with Maggie
• Update methods and results

Killifish Methylation and Expression:

• Test BAT_DMRcorrelating to match RRBS and RNA-Seq data
• Investigate SNP associations with RRBS data
• Look into mQTL analysis
• Start RRBS mapping with new genome
• Update methods and results

Virginica Methylation and Expression:

• Examine connections between transcript counts and methylation
• Determine which hypothesis-driven analyses from the workshop should be incorporated into the paper or redone based on gene expression results
• Finish transcriptional noise analysis
• Return to SPLS

Green Crab Pilot Experiment:

• Analyze survivorship data by treatment and sex
• Analyze time-to-right data by treatment, sex, weight, and integument color
• Determine workflow for respiration data analysis
• Determine workflow for metabolomics sample processing

Other:

• Address reviewer comments on ocean acidification and reproduction review
• Check in about eelgrass transcriptomics paper
• Evaluate projects in deep freeze
• 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.

Hawaii Gigas Methylation:

Once the eelgrass paper is submitted and the Manchester paper is about to be published, 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