September was a doozy. It set the pace for what’s proving to be an absurdly busy fall, between making progress on multiple projects and applying to faculty jobs! Hopefully there’s room for some disco amongst all the panic.

September Goals Recap

Coral Transcriptomics:

• Finalized the differential expression analysis
• Annotated the differentially expressed gene list and started digging through results
• Completed gene enrichment analysis
• Started compiling lists of relevant papers

Killifish Methylation and Expression:

• Completed alignment to the new genome
• Continued the RRBS workflow with the new genome alignments
• Reviewed RNA-Seq data
• Decided against presenting this data at EPIMAR because the methylation story was not clear

Virginica Methylation and Expression:

• Returned to SPLS anlysis…but wasn’t able to get results because of mox issues

Faculty Applications

• Revised my research, teaching, and DEI statements
• Submitted three applications!

Other:

• Finished addressing reviewer comments on ocean acidification and reproduction review. Our review was accepted!

October Goals

Virginica Methylation and Expression:

• Finish SPLS analysis for gene methylation and expression
• Conduct predominant isoform analysis
• Conduct transcriptional noise analysis
• Present results at EPIMAR
• Determine which other hypotheses should be tested

Killifish Methylation and Expression:

• Test BAT_DMRcorrelating to match RRBS and RNA-Seq data
• Conduct pathway analysis for RNA-Seq data
• Investigate SNP associations with RRBS data
• Look into mQTL analysis
• Start RRBS mapping with new genome
• Update methods and results
• Put together APS talk

Green Crab Pilot Experiment:

• Figure out which parts of the analysis Sara and Mikayla can work on
• 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

Coral Transcriptomics:

• Dig into annotated genes
• Conduct WGCNA on the cluster

Other:

• Finish addressing reviewer comments on ocean acidification and reproduction review
• 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 after EPIMAR.

• 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