January 2025 Goals

January 2025 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. e5 ncRNA complete draft of manuscript submit to biorxiv
  2. Pacuta manuscript submit to biorixiv
  3. Resubmit Astrangia review by Jan 15
  4. CBASS results + discussion
  5. Astrangia 2021 miRNA and mRNA DE results

Sample processing

  1. Process e5 timeseries samples for lipids + metabolites by Jan 15
  2. Mcap phys stuff ?

Data analysis

  1. Look into trimming for Mcap data
  2. Double check all Mcap data
  3. CBASS survey + ED50 data

Field work / travel

  1. SICB
  2. Fill out TERs (CBASS and sicb)

Daily log

20250101

  • Working on SICB presentation
  • Rerunning mirdeep2 mapper.pl script for Mcap data

20250102

  • Mcap data analysis - trimming to 35bp for raw data and running mirdeep2 on reads trimmed to 75bp
  • Travel to GA

20250103

  • Mcap data analysis (wgcna for mrna)
  • Working on sicb presentation
  • SICB

20250104 - 20250107

SICB!

20250108

  • Travel to RI
  • Submission of Pacuta paper to biorixiv
  • Prepping submission for molecular ecology

20250109

  • Edits to Astrangia review
  • Some stuff for Apul methylation
  • Emails

20250110

  • Apul methylation plotting

20250112

  • Apul methylation plotting and writing

20250113

  • Helping Zoe and Hollie prep for NYC
  • Astrangia review edits
  • Submitted Pacuta 2022 to molecular ecology
  • Pacuta paper out on biorvix!
  • CBASS edits + vba
  • Email catch up

20250114

  • Lauren meeting
  • Astrangia review edits
  • Therapy

20250115

  • Writing time
  • Lipid metabolite e5 sample prep (6 samples)

20250116

  • Writing with Hollie - Astrangia review

20250117

  • Cutting words for Astrangia review
  • e5 meeting
  • Lipid metabolite e5 sample prep (18 samples)

20250118

  • Resubmitted Pacuta paper (w/ line numbers)
  • Submitted Astrangia review revisions
  • Lipid metabolite e5 sample prep (12 samples)

20250119

  • Submitted epimar abstract
  • Lipid metabolite e5 sample prep (12 samples) - finished!

20250120

Nothing

20250121

  • Shipped e5 samples
  • Picked up dry ice
  • Freezer inventory
  • Aquarium room stuff
  • Resubmitted Astrangia review (data now archived on zenodo)

20250122

  • CBASS paper
  • Skype a scientist
  • reefbites staff meeting
  • Mcap smRNA mirdeep2 miRNA prediction and quantification

20250123

  • Writing meeting
  • Astrangia 2021 miRNA mRNA coding

20250124

  • Astrangia 2021 miRNA mRNA coding
  • Apul genome methylation coding and results writing
  • Reefbites meeting

20250127

  • Astrangia 2021 miRNA mRNA coding
  • Lab meeting
  • Hollie meeting

20250128

  • Astrangia 2021 miRNA mRNA coding and writing
  • Helping Zoe ship corals
  • Helping Flo with coding
  • Therapy

20250129

  • Astrangia 2021 miRNA mRNA coding and writing
  • Prep for switchfree library prep tomorrow
  • Reefbites posting

20250130

  • CBASS meeting
  • Switchfree library prep w/ 13 samples

20250131

  • Writing time
  • e5 meeting
  • Astrangia 2021 miRNA mRNA pathway investigation and writing

How did I do with my goals this month?

Writing and manuscripts

  1. e5 ncRNA complete draft of manuscript submit to biorxiv - no, still on Hollie’s desk
  2. Pacuta manuscript submit to biorixiv - yes!
  3. Resubmit Astrangia review by Jan 15 - yes!
  4. CBASS results + discussion - my section of results pretty much done
  5. Astrangia 2021 miRNA and mRNA DE results - yes, working on writing up results and discussion

Sample processing

  1. Process e5 timeseries samples for lipids + metabolites by Jan 15 - yes and sent to UW facility
  2. Mcap phys stuff ? - no, low priority

Data analysis

  1. Look into trimming for Mcap data - not really since sicb
  2. Double check all Mcap data - not really since sicb
  3. CBASS survey + ED50 data - yes, need to make manuscript ready plots

Field work / travel

  1. SICB - yes! Very fun
  2. Fill out TERs (CBASS and sicb) - nope still need to do this

Overall a very productive month. I met with Hollie earlier this month and we discussed my defending in either April or July (most likely April given committee scheduling). I’m shifting my focus to completing my chapters and lots of writing for the next few months.

Notes:

GSA for maldives ask Hollie for cfs for maldives sicb put difference on intern uber:8.10+10.19+7.29+8.48+10.21+8.95

polyA for Mcap tapestation and qubit for every sample – 32 samples for me, #1-32, ask what concentrations to pool at – will be prepared to pool at specific molarity

  • https://knowledge.illumina.com/library-preparation/dna-library-prep/library-preparation-dna-library-prep-reference_material-list/000001240
Written on January 1, 2025