So…I guess I’m defending this year? My plan is to defend in June, which means I need to start wrapping stuff up and analyzing data! Last quarter I made it through the rest of my adult C. virginica gonad DNA and RNA extractions, and sent my adult C. gigas gonad DNA for WGBS. However…I still have labwork that needs to be finished and libraries that have yet to be sequenced. It’s going to be a busy month (and quarter).

December Goals Recap

Virginica Labwork:

• Finished extracting sperm DNA and RNA!
• Contacted Zymo for a quote but didn’t hear back, so I didn’t send anything for sequencing

Coral Methylation Comparison:

• Updated the methods and results with contingency test information
• Created an experimental design figure
• Contributed to the discussion section
• Finalized manuscript for NOAA internal review!

Other::

• Examined associations between methylation island characteristics and GOterms in overlapping genes in C. gigas
• Put together a SICB talk, including burned on captions!

January Goals

Hawaii Gigas Methylation:

• Trim data
• Run trimmed data through pipeline from the coral paper
• Identify differentially methylated loci associated with treatment and ploidy

Gigas Gonad Methylation:

• Trim data
• Run trimmed data through pipeline from the coral paper
• Identify differentially methylated loci in methylKit
• Determine if there are existing ATAC-Seq datasets that can be used to incorporate chromatin organization information

Virginica Labwork:

• Obtain WGBS and RNA-Seq quotes from Zymo
• Send sample for sequencing!
• Determine if there are any mantle samples that should be used for DNA/RNA extractions

ATAC-Seq Labwork:

• Purchase reagents and identify samples to test cell dissociation protocols
• Ensure protocol is easy to follow and is accessible for the lab
• Dissociate and cryopreserve some cells

Gigas Labwork:

• If there’s some lag time while waiting for ATAC-Seq reagents and analyzing WGBS data, test RNA extraction protocol
• Extract RNA from samples sent for WGBS
• Send RNA for library preparation and sequencing
• Identify location of larval samples for potential extractions