October 2023 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Submit Astrangia review to Coral Reefs
2. Full draft of dissertation proposal
3. Write full methods and results for Astrangia 2021 experiment
4. Continue outlining histology manuscript intro
5. Outline sections for E5 manuscript about descriptive ncRNAs

Sample processing

1. RNA extractions for AH - HI 2023
2. Physiology processing for developmental time series 2023
   • Carbs
   • Lipids
   • Cell counts
3. Initial cell counts for Astrangia 2021
   • Count 20 samples and see how variable they are after homogenizing 2x

Data analysis

1. E5 deep dive - lncRNA and miRNA
2. Astrangia mRNA analysis

Daily log

October 1

• Full review of dissertation proposal

October 2

• Continued to refine proposal
• Aquarium room work, received corals from HI
• Read 2 papers
• Writing meeting
• Lab journal club
• Worked on glmmSeq and DESeq2 code

October 3

• Met w/ Hollie about proposal
• Ran plate of carbs
• Worked on DESeq analysis of Astrangia mRNA

October 4

• Got DESeq code to work by grouping treatment and timepoint into one ‘group’. Still want to investigate if I can build a model with the design ~Treatment + Timepoint + Treatment:Timepoint
• Tried to get bowtie to work on Andromeda, did not succeed
• Ran orthofinder for e5 species (protein seqs) and did a orthogroup blast comparison for e5 deep dive
• Read papers on mechanisms of miRNAs responding to stress

October 5

• Extracted 3 AH samples using elution volume of 65 uL
• Tapestation on 5 of AH samples that failed Qubit
• Reviewed LZ and CG docs
• Worked on IDP

October 6

• Worked on flexbar smRNA code
• Meeting w/ Hollie
• e5 meeting
• Moved samples out of failing -80C
• Lab meeting
• it my bday

October 7

• RNA QC comparisons
• Working on quals materials

October 8

• Working on quals materials

October 9

• Helped Taylor collect corals at Fort Wetherill
• Organized quals materials
• Ran QC for trimmed miRNAs

October 10

• RNA Qubit tests on AH samples
• Worked on qualifying exam presentation
• Led DIBP workshop

October 11

• Worked on qualifying exam presentation
• Spoke w/ Rachel’s class
• Went through sediment stress manuscript and listed out questions that I might get asked

October 12

• Worked on qualifying exam presentation
• Worked on adding supplementary materials for presentation
• Received Zymo kits!!!!

October 13

• Worked on qualifying exam presentation
• Made reagents for Zymo kits
• Lab meeting
• Colloquium

October 14

• Worked on orthogroup + GO term sheets

October 15

• Prepped for quals

October 16

• Prepped for quals
• Writing meeting

October 17

• Prepped for quals
• Ariana + Hollie meeting
• ReefBites meeting

October 18

• Prepped for quals
• Aquarium room

October 19

QUALS!

October 23

• Organized SMART goals and a daily plan for the semester (with a focus on comps reading)
• Worked on Astrangia review manuscript (intro, research recs, knowledge synthesis)
• Updated figures for Astrangia review manuscript

October 24

• Extractions for AH
• F1F2 meeting
• Located Pacuta spat from HI 2022 - sending for sequencing tomorrow

October 25

• SUBMITTED ASTRANGIA REVIEW PAPER!! to Coral Reefs
• Aliquotted samples for sequencing (HI 2022 samples)
• Remade daily measurement script for CBLS wet lab

October 26

• Prepped for comps
• Started to arrange notion pages for studying

October 27

• Practice extraction w/ Chloe
• E5 all hands meeting
• Lab meeting
• Some aquarium room stuff

October 28

• Read 2 chapters of flexible phenotype

October 29

• Extraction for DB samples
• Wrote up extraction posts

October 30

• Extractions
• ncRNA e5 meeting
• Aquarium room duties

October 31

• Prepped for comps
• Set up shipment for Federica and Danielle samples to Genewiz