April ‘23 Goals

April ‘23 Goals

Primary Focus

DNA/RNA Extractions & Qubit!

• Currently waiting to receive the ‘Mortexer’ … can’t do extractions until we get that instrument!
• 1st round:
  • 1-Ea
  • 2-Ea
• 2nd round:
  • 1-CAa
  • 1-CHa
  • 1-LAa
  • 1-LHa
  • 1-HAa
  • 1-HHa
  • 1-OAa
  • 1-OHa

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Sequencing Quotes Results

Quotes are for library prep & sequencing

16S

• data format - raw FASTQ files

RNA-seq

• The size of the Montipora capitata genome is 614.5 million base pairs.

• Illumina, 2x150bp (for gene expression profiling)

• poly-A RNA selection

• 15-20 million raw paired-end reads per sample

• data format - raw FASTQ files

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• UW Northwest Genomics Center (email sent 05APR2023)

• Azenta Life Sciences (previously Genewiz)

  • sequencing platform:

  • RNA-seq, 10 samples: 23-25 business days, 15-20 million reads per sample, PolyA selection for mRNA, ERCC spike-in, $180 per sample with promo, $1800 total pre-tax

  • 16S, 10 samples: 20ng/uL DNA concentration, 25uL volume, $95 per sample, $950 total pre-tax

• Univ. of Texas Austin Genomic Sequencing Analysis Facility (GSAF)

  • sequencing platform: MiSeq V2

  • GSAF uses BaseSpace for NGS Illumina data delivery, If you do not have an account, please sign up for one here.

  • $260.39 per sample RNA-seq library prep with poly(A) enrichment

  • RNA-seq, 10 samples, $32,642.71🤯

  • Tag-seq, 20 samples $1,500 ($75 per sample, must be sent in 96-well plate)

• Mr. DNA Lab (email sent 05APR2023)

  • RNA-seq, $580 per sample

  • 16S, $75 per sample + $100 library prep fee

• FYR Diagnostics (email sent 05APR2023)
  • They do not do RNA depletion/poly(A) enrichment… instead they use a Watchmaker genomics library prep for target enrichment applications
• University of Oregon Genomics Center

  • RNA-seq, $255 per sample, (does not include poly(A) enrichment! 1 to 100ng of purified total, polyA enriched RNA in 10uL of RNase-free water or buffer

  • 16S v3-v4 region, $1,400 per plate of 95 samples, any amount of pure DNA (more = better) in at least 30uL volume

Send off Samples for Sequencing Service

• pick quote provider
• send for sequencing ( 2-4 weeks )

FISH 546 in SP23

• prepare scripts to do RNA-seq differential gene expression analysis in-class
• use ‘fake data’ from publicly available M. capitata RNA-seq data

Supporting Roles

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

• Ongoing participation in Student Advisory Council

• Ongoing mentoring with IBIS mentee Nora Hessen

  • laboratory work! do DNA/RNA extraction together

Looking Ahead…

Spring 2023

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 10th: FHL Marine Botany TAship starts at Friday Harbor Labs!
• begin drafting manuscript(s)

July

• July 15th: FHL Marine Botany TAship ends!
• continue drafting manuscript
• continue bioinformatics pipelines

Aug

• continue drafting manuscript
• continue bioinformatics pipelines