I had really lofty goals for August without realizing that I was going to be visiting family for a good chunk of the month (aka decreased productivity). I made some headway on things, but most of these goals will rollover to make a very packed September.

August Goals Recap

Coral Transcriptomics:

• Completed initial TagSeq mapping but not differential expression analysis
• Haven’t written methods or results

Killifish Methylation and Expression:

• I revisited the RNA-Seq results but did not get a chance to do anything else

Virginica Methylation and Expression:

• Lots of great discussions but no actual work was done

Green Crab Pilot Experiment:

• Cleaned and analyzed the HOBO data to ensure my temperature treatments were significantly different!

Other:

• Started addressing reviewer comments on ocean acidification and reproduction review
• Checked in about eelgrass transcriptomics paper and confirmed I don’t have any work to do with that paper
• Evaluated projects in deep freeze…they’re oging to stay there a bit longer
• Found relevant faculty positions I will apply to this cycle

September Goals

Coral Transcriptomics:

• Finalize differential expression analysis
• Complete gene enrichment analysis
• Update methods and results
• Outline discussion

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 draft EPIMAR talk

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:

• 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

Faculty Applications

• Sign up for academic jobs workshop
• Revise research statement
• Revise teaching statement
• Revise DEI statement
• Revise cover letter
• Update CV
• Submit applications due in September and early October

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