With the amount of work I need to get done this short month, I’m definitely on the meow meow train. But I think at the end of this month, I’ll have a much clearer understanding of how much work is left for me before I’m solely in an analysis and writing phase, and when may be a reasonable time to defend!

January Goals Recap

Hawaii Gigas Methylation:

• Trimmed data! Also dealt with overrepresented poly-G sequences in my samples by trimming three times total.
• Ran trimmed data through pipeline from the coral paper through bismark! Forgot that this takes a while so I wasn’t able to complete any other steps.
• Investigated DSS as a potential package for identifying differentially methylated loci with multiple experimental conditions

Gigas Gonad Methylation:

• I didn’t get any of my data until last week, so I haven’t touched it yet!

Virginica Labwork:

• Obtained WGBS and RNA-Seq quotes from Zymo
• Started getting PO numbers for each quote
• Was not able to send samples for sequencing since I don’t have both PO numbers
• Did not determine if there are additional samples that should be extracted sequenced

My plate was pretty full with bioinformatic analyses and quarantining after getting back from California, so I didn’t make any progress on ATAC-Seq Labwork or Gigas Labwork!

February goals

Hawaii Gigas Methylation:

• Evaluate bismark output using coral methylation workflow
• Complete preliminary assessment of DML with methylKit
• Try identifying DML with DSS
• Compare methylKit and DSS DML output and determine which approach is suitable
• Determine genomic location of DML
• Identify significantly enriched GOterms associated with DML
• Identify methylation islands and non-methylated regions
• Locate an ATAC-Seq dataset that could be used to practice integrating chromatin information with methylation
• Start drafting manuscript

Gigas Gonad Methylation:

• Trim samples
• Align samples with bismark and evaluate output
• Identify DML using either methylKit or DSS
• Determine genomic location of DML
• Identify significantly enriched GOterms associated with DML
• Identify methylation islands and non-methylated regions
• Decide if it’s worth extracting gonad RNA for integrated RNA-Seq and methylation analyses
• Start drafting manuscript

Virginica Labwork:

• Send samples for sequencing!

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

Other:

• Continue work on ocean acidification and reproduction review in order to submit the manuscript this quarter
• Complete review for Molecular Ecology
• Watch SICB talks and prepare for live discussion session