Fall is in full swing! I focused on analyses for different conference presentations this month.

October Goals Recap

Virginica Methylation and Expression:

• Conducted SPLS analysis for gene methylation and expression without tuning
• Conducted predominant isoform ad transcriptional noise analyses, and found some interesting results!
• Presented results at EPIMAR!

Killifish Methylation and Expression:

• Reviewed methylation landscape analysis
• Didn’t test BAT_DMRcorrelating to match RRBS and RNA-Seq data because only one DMR was located in a gene, and that gene was not differentially expressed
• I was missing information to conduct the pathway analysis, so I looked at HIF and AHR pathways instead
• Tracked down SNPs information for populations, but couldn’t find pre-existing SNP information for Scorton Creek
• Gave a talk at the APS Comparative Physiology Conference!

Green Crab Pilot Experiment:

• Emailed Sara and Mikayla to determine which parts of the analyses they were interested in working on

Other:

• THE OCEAN ACIDIFICATION AND REPRODUCTION REVIEW IS PUBLISHED!

November Goals

This month, I want to focus on postdoc projects so I can work towards getting a publication ready soon.

*Coral Transcriptomics:

• Run a WGCNA
• Dig into gene functions for assigned categories
• Update methods and results

Killifish Methylation and Expression:

• Continue BAT workflow with new genome
• Conduct formal pathway analysis for RNA-Seq data
• Review existing lab data
• Determine protocol for SNP identification
• Conduct in silico RRBS digestion
• Characterize DEG that overlap between populations
• Quantify gene expression variability
• Visualize DEG data

Green Crab Pilot Experiment:

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

Other:

• Review supplementary material for eelgrass transcriptomics paper
• Distribute results of postdoctoral mentorship experiences survey
• Launch the postdoctoral mentoring program

Deep Freeze

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

Hawaii Gigas Methylation:

I will revisit this paper in December.

• 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 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