August 2024 Goals

August 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. Dissertation proposal submission to grad school
  2. Complete Pacuta 2022 manuscript edits and send to co-authors
  3. Resubmission of Astrangia review
  4. e5 ncRNA intro and results
  5. Write postdoc blurbs and send

Sample processing

  1. Send Mcap 2023 samples for sequencing
  2. Re-amp 6 WGBS e5 deep dive samples
  3. Clip and re-extract 8 samples for e5
  4. Find and send RNA samples for e5
  5. WGBS library prep for e5 samples
  6. Phys stuff for AST and Mcap DT ?

Data analysis

  1. 3’UTR for AST 2021 and rerun miRanda with that info
  2. Apul methylation

Field work / travel

  1. Submit BIOS TAR
  2. Check out dive at URI

Daily log

20240801

  • Adding 2024 papers to Astrangia review
  • Genohub request
  • Renewed DAN
  • Reading about pacbio hifi methylation
  • Started running ccs-kinetics-bystrandify

20240802

  • Aquarium room stuff
  • Installed jasmine
  • Clipped coral for extractions

20240805

  • E5 extractions + QC
  • Aquarium room stuff
  • Signed up for classes
  • Weekly updates
  • Random admin stuff

20240806

  • Started pico prep with 6 e5 samples that previously failed
  • Shipped a bunch of stuff
  • Aquarium room stuff
  • Minor writing

20240807

  • Rest of pico prep with 6 e5 samples + QC
  • Submitted timesheet on ecampus
  • Submitted biology letters reply

20240808

  • Got into cbass workshop
  • Pacuta paper writing, mostly discussion
  • Aquarium room stuff

20240809

  • Aquarium room stuff
  • e5 meeting
  • Pacuta / e5 ncRNA paper writing
  • Remaking Astrangia review figs

20240812

  • Prepping data for gene ext AST
  • Installing gene ext
  • Aquarium room stuff
  • Results writing for AST 2021 paper

20240813

  • Updating gene ext installation
  • Adding papers for Astrangia review, updating figures, formatting

20240814

  • Checkout dive
  • Editing Astrangia review for word count
  • Submitted to biorxiv

20240815

  • Cleaned out muffle furance
  • Submitted review to OSF preprints
  • Edits to Pacuta paper, organized refs
  • Organizing things for e5 samples
  • Organizing github things
  • Sent Pacuta manuscript to co-authors again
  • TER things
  • Confirmed cbass workshop

20240816

  • e5 extractions
  • e5 organization
  • e5 RNA aliquoting into plates - will send for sequencing on Monday

20240818

  • Adding stuff to NSF report
  • Updating results in Apul genome paper
  • SICB abstract
  • Reading about DREM/playing around with GUI

20240819

  • Sent RNA
  • Genohub requests for Mcap samples
  • Bermuda TER resubmitted
  • Looking at e5 DNA stuff
  • Cleaned aquarium room
  • Wrote sicb abstract and sent to co-authors
  • Tried and failed to load gene ext
  • Danielle meeting
  • bedtools closest coding for e5

20240820

  • Getting sample lists ready for genohub - mcap 2023 libraries
  • bedtools closest coding for e5
  • Therapy
  • Adding to NSF report
  • Looking into circos plots

20240821

  • Check out dive
  • Lab meeting

20240822

  • Grad tour thing
  • Discussion for ncRNA e5 paper

20240823

  • e5 ncRNA closest genes to ncRNAs
  • e5 meeting

20240824

  • Proximity for miRNAs e5 ncRNAs - running into issues with Apul
  • Submitted SICB abstract

20240825

  • Admin life stuff

20240826

  • Cleaned up miRNA libraries
  • Organized and shipped libraries for sequencing - Mcap 2023 DT project
  • Hollie meeting + summary
  • Results and discussion e5 ncRNA
  • Looking at function of closest mRNA to miRNA

20240827

  • Found test metabolomic samples for e5
  • First part of pico prep
  • Therapy
  • Thinking about postdoc stuff

20240828

  • Rest of pico prep + QC
  • Lab meeting
  • Prep for science saturday

20240829

  • Airbrushed and separated fractions for metabolomics test
  • Discussion e5 ncRNA
  • Started running shortstack
  • Attempting to install gene ext AGAIN
  • Filled out dibp form
  • Ran fuzznuc + looked at output

20240830

  • Looking at shortstack output
  • Ben meeting
  • Sending post doc emails
  • 2 dives for Astrangia collection

20240831

  • Thinking about postdoc things
  • Finishing stuff for NSF report

August reflection

How did I do with my goals for this month?

Writing and manuscripts

  1. Dissertation proposal submission to grad school - nope lol
  2. Complete Pacuta 2022 manuscript edits and send to co-authors - yes! On desks of HP, TM, and AH
  3. Resubmission of Astrangia review - yes! Currently in review at Biology Letters
  4. e5 ncRNA intro and results - yes! Waiting on lncRNA stuff
  5. Write postdoc blurbs and send - sort of! Emails have been sent

Sample processing

  1. Send Mcap 2023 samples for sequencing - yes!
  2. Re-amp 6 WGBS e5 deep dive samples - tried a few times but unsuccessful. Need to nanodrop DNA and libraries before next steps
  3. Clip and re-extract 8 samples for e5 - yes
  4. Find and send RNA samples for e5 - yes
  5. WGBS library prep for e5 samples - no, decided to send them out for library prep
  6. Phys stuff for AST and Mcap DT - no

Data analysis

  1. 3’UTR for AST 2021 and rerun miRanda with that info - no, having issues with installing gene ext
  2. Apul methylation - sort of? ran fuzznuc which identified CpG motifs in assembled genome

Field work / travel

  1. Submit BIOS TAR - yes
  2. Check out dive at URI - yes

Pretty happy with all that I accomplished in August! Things are moving forward.

Written on August 1, 2024