Break? Over. Rest? Acquired. Projects? Ready to be tackled.

Me? Not ready to work yet but oh well here we go.

I have some lofty goals this month, but my plan is to try and split my time more effectively between my PhD and postdoc projects. I think I’ll work a couple days at home and dedicate those to PhD projects, and spend my office days working on postdoc projects. Hopefully the physical separation will help me compartmentalize the work so I don’t feel guilty for not working on postdoc projects while working on my PhD projects, and vice versa!

November Goals Recap

Gigas Gonad Methylation:

• SO CLOSE to finishing reworking the discussion! But also not done. Whoops.

Hawaii Gigas Methylation:

• I didn’t have time to work on the Hawaii paper, but now that I have Rajan’s feedback I can start to incorporate that as I restart my work

Virginica Gonad Methylation:

• Talked through methods with Steven and Sam
• Have yet to extract SNPs or perform any actual analysis myself

Coral Transcriptomics:

• Decided on an extraction protocol and tested the extractions
• Tested the extractions again using different starting volumes. It did not go well, but I have a plan to move forward!
• I put a hold on metatranscriptomics methods until I could figure out how to successfully extract coral RNA. You know, baby steps.

NSF PRFB:

• Successfully wrote and submitted my NSF PRFB!

Other:

• Finished identifying new papers for ocean acidification and reproduction review
• Completed Molecular Ecology review
• Identified a killifish RRBS and RNA-Seq dataset to work on with Neel
• Discussed potential projects involving DNMT-3 knockout zebrafish or menhaden with Neel

January Goals

Gigas Gonad Methylation:

• FINALLY finish the discussion
• Revise the introduction and abstract
• Send to Steven for edits
• Submit to a journal and bioRXiv

Hawaii Gigas Methylation:

• Address Rajan’s edits
• Review DSS script and determine if I should go back 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

Virginica Gonad Methylation:

• Update methods of draft paper
• Extract SNPs with BSnper and EpiDiverse
• Identify methods for linking WGBS and RNA-Seq data
• Identify lncRNA and miRNAs in dataset

Coral Transcriptomics:

• Continue testing extraction protocol to identify a successful methods
• Use gel to check RNA integrity
• Extract all A. cervicornis samples

Killifish Methylation and Expression:

• Review BAT mapping and DMR identification protocol
• Start mapping procedure for methylation data
• Identify protocol for RNA-Seq data

Ocean Acidification and Reproduction Review:

• Start integrating new papers into main text and supplemental material
• Revise figures

Other:

• Meet with Carolyn, Ann, and Neel to discuss projects and funding opportunities for the next six months
• Develop any potential projects
• Coordinate postdoctoral mentoring program with Maggi