March ‘23 Goals

March ‘23 Goals

Primary Focus

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

  • pipettes serviced by gilson rep end of Feb ‘23

• Protocol dry-run walk-thru with IBIS mentee

  • dry-run walk-thru on 30MAR23

  • samples located in ‘sucks’ -80 freezer, top shelf, far back right corner

• 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?

    • start with a practice of 2

    • follow-up with 8 more (total of 10 preps in kit)
    • buy 50-prep kit and continue if extractions went well
• UW Northwest Genomics Center
• Azenta Life Sciences (previously Genewiz)
• Univ. of Texas
• Mr. DNA Lab
• FYR Diagnostics (20% off promo)

Send off Samples for Sequencing Service

• finalize extraction strategy (how many samples, from which treatments)
• pick quote provider
• 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 )

Start FISH 546 in SP23

• setup Linux Subsystem for Windows in preparation of Bioinformatics Course
• receive sequences and prepare to do analysis in-class

Supporting Roles

• Complete SMEA/FISH 539 coursework WI23

• Start FISH 546 coursework SP23

• Ongoing coordinating for GSIS speaker Dr. Nicola S. Smith

• Ongoing participation in Student Advisory Council
  • CoEnv Assistant Dean of Diversity Equity & Inclusion (ADDEI) hire student input
• Ongoing mentoring with IBIS mentee Nora Hessen

  • brainstorming & meeting every Wednesday for 2hrs

  • laboratory work! do DNA/RNA extraction together

Looking Ahead…

Spring 2023

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

Advisor Recommendations