June 2024 Goals

June 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

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

Sample processing

  1. miRNA library prep for 24 Mcap DT 2023 samples
  2. WGBS library prep for e5 deep dive samples (15 samples)
  3. Phys stuff for AST and Mcap DT ?

Data analysis

  1. Work on functional analysis of miRNA target genes for AST 2021
  2. Complete Apul mito assembly
  3. Complete Apul assembly

Field work / travel

  1. Help Flo get experiment started at BIOS
  2. Research diving course at BIOS (June 23 - July 13)

Will be taking a vacation in NJ with family from July 14-20.

Daily log

20240603

  • Confirmed dive gear order
  • Edited Pacuta manuscript
  • Organized Pacuta supplementary tables
  • miRNA library prep section 1
  • ncRNA paper writing and organizing
  • Sent Pacuta manuscript to coauthors for edits woo
  • BIOS paperwork
  • Citations for Pacuta paper

20240604

  • miRNA library prep sections 2, 3, 4 + QC
  • Picked up diving paperwork
  • Responded to e5 github issue
  • ncRNA e5 results writing
  • updated Pacuta plots

20240605

  • Dr appt
  • Re-amplifying miRNA libraries + QC
  • ncRNA results writing
  • Lab meeting
  • Hollie meeting
  • Aquarium stuff
  • Lead class!

20240606

  • Looked for more Astrangia papers for lit review
  • Wrote up notebook posts from yesterday
  • Bead cleanup for miRNA libraries + QC
  • Remaking Astrangia review figures
  • Edits for Pacuta paper
  • Making new figures for Pacuta paper
  • Rerunning DESEq2 code w/ new pOverA

20240607

  • Editing Pacuta 2022 paper + making new figs, updating results
  • miRNA library prep all sections + QC

20240608

  • Editing Pacuta 2022 paper + making new figs, updating results
  • Blasting Pacuta genes

20240610

  • Biology letters questions
  • Tried again to install mitohifi
  • Called John re diving gear
  • Called zymo
  • Edits for Pacuta
  • Pacuta environmental stats table

20240611

  • Worked on Bio letters responses
  • Pacuta discussion + intro + coding
  • Genome meeting w/ Ross, Hollie & Trinity
  • Fought with MitoHifi

20240612

  • First part of section 1 for Pico prep - e5 deep dive samples
  • Helped Zoe with stuff
  • IGB looking on my AST stuff

20240613

  • Packing
  • Pico library prep w/ e5 deep dive samples

20240614

  • Meeting w/ Ariana
  • e5 ncRNA meeting
  • Therapy
  • Packing

20240615

  • Travel to Bermuda
  • IDing Apul 3’UTRs for deep dive

20240616

  • IDing Apul 3’ ends + starting Apul miranda run
  • IDing Peve 3’ ends + starting Peve miranda run

20240617

  • Assigning 3’UTRs with genes and looking at miranda output for Apul
  • Setting up Flo experiment
  • Blasting sym genomes against hifi reads

20240618

  • Setting up Flo experiment

20240619

  • Contamination clean up for Apul genome
  • Made OSF for Apul genome
  • Setting up Flo experiment

20240620

  • Setting up Flo experiment

20240621

  • Setting up Flo experiment

20240622

  • Looking over dive course materials
  • Updating functional annotation script for Pacuta 2022
  • Looking at mitohifi output and blasting final mito fasta against hifi reads
  • Removing contam from hifi reads

20240623

  • Starting hifiasm assembly with clean hifi reads
  • Setting up Flo experiment

20240624

  • RDM course
  • Flo sampling

20240625

  • RDM course
  • Trying to make some plots bleh

20240626

  • RDM course
  • Assembly finished running!

20240627

  • RDM course
  • Assembly QC

20240628

  • RDM course

20240629

  • RDM course

20240630

  • RDM course
  • Assembly scaffolding code

June reflection

How did I do with my goals for this month?

Writing and manuscripts

  1. Dissertation proposal submission to grad school - nope. Hollie and I met about it but she has not looked at it yet
  2. Complete Pacuta 2022 manuscript and send to co-authors for edits - yes! Co-authors were very prompt in responding and we decided to rework the framing of the story so that we are focusing more on the variability of synergistic stressors. Also had to rerun some code
  3. Resubmission of Astrangia review - nope, really need to do this
  4. e5 ncRNA results - yes for the protein machinery and the miRNAs. Waiting on Zach and Javi for the lncRNAs and piRNAs, respectively

Sample processing

  1. miRNA library prep for 24 Mcap DT 2023 samples - yes! Ran into some issues with the taq premix. I was able to re-amp 12 samples but I ran out of good taq premix for the final 12. Zymo should be sending me some replacement mix soon
  2. WGBS library prep for e5 deep dive samples (15 samples) - yes! 6 did not amplify, need to redo
  3. Phys stuff for AST and Mcap DT - nope, no time

Data analysis

  1. Work on functional analysis of miRNA target genes for AST 2021 - nope
  2. Complete Apul mito assembly - yes!
  3. Complete Apul assembly - yes!

Field work / travel

  1. Help Flo get experiment started at BIOS - yes!
  2. Research diving course at BIOS (June 23 - July 13) - yes! A week in

Overall, got a lot done this month!

Written on June 3, 2024