Feb ‘23 Goals
February ‘23 Goals
Primary Focus
Conduct 1st Committee Meeting
- Write committee agreements (complete on 01FEB23)
- Build ‘committee presentation’ blog post (here) (complete on 05FEB23)
- Host meeting (complete on 06FEB23)
- Integrate feedback into master’s thesis committee meeting #1 blog (complete on 07FEB23)
DNA/RNA Extraction Protocols
- Research DNA/RNA extraction kits (compete on 05FEB23)
- Buy Quick-DNA/RNA Miniprep Plus Kit , 10 preps ($106.70, requested 08FEB23 on Hall Grant Budget)
- Receive kits (complete on 23FEB23)
- Draft protocol (complete on 15FEB23 )
- Locate (… or buy or borrow) 300uL/500uL & 1000uL pipettes & tips
- Protocol dry-run walk-thru with IBIS mentee
- Edit/amend protocol
- Trial methods with subset of samples Note: We originally thought about using Callum’s coral fragments for the trial, but these were not held at -80C, and therefore the RNA step would not work properly
Get Sequencing Quotes
- Get general idea of costs ( $80/sample for 16S & $200/sample for RNAseq )
- Answer/identify common quote questions:
- What type of library prep is needed?
- What is the minimum number of reads per sample?
- How many samples to sequence?
- UW Northwest Genomics Center
- Azenta Life Sciences (previously Genewiz)
- Univ. of Texas
- Mr. DNA Lab
- FYR Diagnostics (20% off promo)
Supporting Roles
- Complete SMEA/FISH 539 coursework
- Ongoing coordinating for GSIS speaker Dr. Nicola S. Smith
- Ongoing participation in Student Advisory Council
- CoEnv Strategic Planning student working group
- CoEnv Assistant Dean of Diversity Equity & Inclusion (ADDEI) hire student input
- Ongoing mentoring with IBIS mentee Nora Hessen
- develop project (DNA/RNA extraction & alpha & beta diversity analysis!)
- lab training & certificates
- brainstorming & meeting every Wednesday for 2hrs
- Apply for FHL Marine Botany TAship
- Apply for WSG Grad Student Assistant, locally sourced seafood project
Apply for PCC Climate Solutions Project Funding
$5k max for solutions-based projects, capstone programs (IBIS), outreach efforts with community organizations and partners. Can be used for Financial Support, Training, Publication & Travel. Rolling application. Would like to apply for this to be used to help IBIS mentee, via more sequencing or publication? Need to brainstorm how to angle ‘solutions-based’ project.
Looking Ahead…
Spring 2023
March
- pick a sequening service
- finalize extraction strategy (how many samples, from which treatments)
- extract DNA/RNA from samples Note: this will be a subset of samples, likely the control vs. highest treatments
- send for sequencing ( 2-4 weeks )
- setup Linux Subsystem for Windows in preparation of Bioinformatics Course
- March 27 Spring Quarter begins : Dr. Robert’s Bioinformatics Course
April
- receive trial sequences
- analyze the sequences in Bioinformatics course
- 2nd round DNA/RNA extraction, & send for sequencing
May
-
analyze sequences with Nora for IBIS project (QA/QC… both run same analysis and see if we get same result?)
- Celebrate IBIS mentee project completion
- assess how we proceed with extraction & sequencing (did we see something interesting to warrant paying for more sequences? do we need to think about finding additional funding to pay for more sequencing?)
- continue bioinformatics pipelines
Summer 2023
June
- June 9th Spring Quarter ends
- June 20th Summer A term begins
- FHL Marine Botany TAship?
- begin drafting manuscript(s)
July
- July 19th Summer A term ends
- continue drafting manuscript
- continue bioinformatics pipelines
Aug
- continue drafting manuscript
- continue bioinformatics pipelines
