May Goals Recap

Pilot Green Crab Experiment:

• Submitted the manuscript to JEB and bioRXiv!

West Coast Green Crab Experiment:

• Determined that the transcriptome assembly itself needed some work. Dug into options for revising the transcriptome assembly
• Restarted transcriptome assembly

MMEP Lab:

• Worked with Ashray evaluate the use of DESeq2 vs. edgeR for DEG analysis
• Finalized experimental design for Mikaela, Emma, and Clara
• Trained Sasha and Noemi on PCR, restriction digests, and gels

Other:

• Completed accessibility for Module 3 and 4 content
• Gave seminars at Stanford and SFSU
• Nancy and I went back and decided to code some different questions instead, since the ones we worked on were very convoluted. We created three new codebooks based on coding the first 25 entries of 3 different questions. I then used our codebooks on the next 50 entries.

July Goals

West Coast Green Crab Experiment:

• Finalize transcriptome assembly parameters based on testing
• Generate and filter revised count matrix
• Remove contaminated sequences from transcriptome
• Annotate transcriptome
• Add metabolomics figures to the draft manuscript
• Write transcriptomic methods

MMEP Lab:

• Create lab handbook
• Update SCU website with brief information
• Photos and bios of undergraduate members on website
• Update recruitment information on website
• Set up recirculating seawater system and start experiments
• Finalize citrate synthase and DNA methylation assay protocols

Hawaii Gigas Methylation:

• Update bismark methods and results
• Revise methylKit analysis and update methods and results
• Integrate ATAC-Seq data
• KOG metaanalysis of existing Crassostrea methylation data
• Revise discussion

** NSF IOS Grant**

• Revise one-pager
• Talk to a program officer
• Identify the correct NSF program and read the solicitation
• Draft research plan
• Draft objectives and significance
• Draft intellectual merit
• Draft broader impacts

Deep Freeze

Things that are not immediate enough to be on the backburner, so they’re stuck in the deep freeze.

Coral Transcriptomics:

These are things I need to do and can probably knock out in a week, but I think they’re a lower priority right now for me since there’s more momentum on other projects. At the very least, I need to reach out to collaborators and get this going again.

• Revise abstract
• Write discussion
• Write introduction