May 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Full draft of dissertation proposal
2. Write physiological results for Astrangia 2021 experiment
3. Resubmit Astrangia review manuscript
4. Begin results for e5 ncRNA paper

Sample processing

1. Extractions + ribofree library prep for 24 Mcap DT 2023 samples
2. Library prep for WGBS (27 samples)
3. Carbs for DT samples
4. Phys (carb, protein, etc) for any remaining AST 2021 samples

Data analysis

1. Finish stats + plots for AST 2021 phys data
2. WCGNAs with mRNA, miRNA and lnRNAs
3. Finish stats for Astrangia 2021 phys data (carbs)
4. Complete Astrangia 2021 mRNA functional enrichment analysis
5. Run miranda with genes of interest, invoking strict seed binding
6. Assemble mito genome for Apul
7. Assemble coral genome for Apul
8. Run miranda with lncRNAs
9. Run DEG analysis with lncRNAs

Daily log

20240501

• Cleaning up old histology stuff
• Lab meeting
• Random lab things
• Labeled tubes for extraction tomorrow
• Started going through lab notebooks for AST 2021 samples
• Started Pacuta SRA submission

20240502

• Extractions + QC for 12 Mcap DT samples
• Aquarium room stuff
• Maggie thesis defense!!
• Locating samples for nanodrop tomorrow
• Continuing SRA submission

20240503

• Nanodropped my Mcap samples + POC samples
• e5 ncRNA meeting
• Other random lab stuff

20240505

• Tried to read about WGCNA
• Helped Zoe w/ HI site selection
• Filled out fellowship google form for Weds meeting
• Dissertation proposal
• Working on Pacuta 2022 discussion
• Uploaded Pacuta 2022 seqs to NCBI
• Updating seq inventory

20240506

• Random lab stuff
• Assisting Zoe
• Aquarium room duties
• Pacuta paper writing
• miRNA mRNA correlation coding!!!!! Exciting
• e5 ncRNA protein machinery muscle alignment with all species

20240507

• Put mercuric chloride waste into waste pickup bottles for the Pacuta 2022 HI project and some of e5; scheduled waste pick up
• Writing biology letters reply
• Allyson defense
• Therapy
• miRNA coding

20240508

• Qubit HS with my samples + POC samples
• Lab meeting / organization
• Zoe LCM
• Fellowship meeting
• Thought about ITS2 concentrations
• Reefbites posting

20240509

• Test ITS2 amp + QC
• Pacuta discussion writing

20240510

• Aquarium room stuff
• Prepped pipettes for calibration
• Pacuta blasting genes of interest

20240511

• Pacuta volcano plots
• looking at blast results

20240513

• Dentist appt
• ITS2 amp + QC
• mirtarrnaseq coding
• Pacuta writing

20240514

• ITS2 amp + QC
• mirtarrnaseq coding
• Hollie meeting
• Aquarium room stuff

20240515

• ITS2 checking amp, bead cleanup + QC
• Lab meeting
• mirtarrnaseq coding and looking into results

20240516

• Meeting updates, notebook posts
• mirtarrnaseq coding and looking into results
• SMART goals
• Filled out ICRS SECC stuff
• Started presentation for temperate coral conference

20240517

• Trinity defense
• e5 meeting
• HI SAP report
• mirtarrnaseq coding and looking into results
• Blasting sig corr genes against ncbi nt + nr db

20240520

• Downloading blast results to computer
• Plating samples for ITS2 sequencing
• mirtarrnaseq coding and looking into results

20240521

• Dissertation proposal writing
• Dropped ITS2 samples off for Janet
• mirtarrnaseq coding and looking into results
• undergrad meeting

202405222

• Lab meeting
• Worked on astrangia presentation
• Aquarium room stuff
• Brief chat w/ Hollie - ordered miRNA prep kits
• Prepped stuff for library prep tomorrow

20240523

• Ribofree library prep sections 1-3
• Diluted primers for library prep
• Worked on AST presentation + coding
• Edited Pacuta 2022 paper

20240524

• Ribofree library prep section 4
• Temperate coral practice talks
• Talk prep

20240526

• Edits to AST plots
• Working on talk

20240527

• Ribofree library QC
• Ribofree library prep sections 1-4 + QC round 2
• Trying to install mitohifi
• Pacuta paper edits

20240528

• Working on presentation
• Dr appt
• Shipped stuff to Ross
• Met w/ Hollie
• Therapy
• Emails

20240529

• Temperate coral conference!

20240530

• Temperate coral conference!
• TAR for Bermuda 2024

20240531

• Tired
• Dr appt
• Submitted TER for temperate coral conference
• Called scuba store re reg, octopus, gauages and BCD
• e5 meeting
• Naming and organizing e5 ncRNAs
• Making figures for e5 paper

May reflection

How did I do with my goals for this month?

Writing and manuscripts

1. Full draft of dissertation proposal - yes, sent to Hollie for edits
2. Write physiological results for Astrangia 2021 experiment - nope
3. Resubmit Astrangia review manuscript - no. Need to wrote the Bio letters response to editor and make some edits to the review itself based on Temperate coral conference
4. Begin results for e5 ncRNA paper - yes! Starting to write the miRNA results + make figures

Sample processing

1. Extractions + ribofree library prep for 24 Mcap DT 2023 samples - yes
2. Library prep for WGBS (27 samples) - no
3. Carbs for DT samples - no, maybe train undergrads ?
4. Phys (carb, protein, etc) for any remaining AST 2021 samples - no, still need to look through master sample list

Data analysis

1. Finish stats + plots for AST 2021 phys data - yes for the most part. Need to discuss w/ Hollie about how to incorporate site maybe as a random variable
2. WCGNAs with mRNA, miRNA and lnRNAs -
3. Finish stats for Astrangia 2021 phys data (carbs) - yes for the most part. Need to make sure all samples are processed
4. Complete Astrangia 2021 mRNA functional enrichment analysis - yes
5. Run miranda with genes of interest, invoking strict seed binding - yes
6. Assemble mito genome for Apul - no, working on installing mitohifi
7. Assemble coral genome for Apul - have the code for it but still need to remove mito reads. Once I assemble the mito genome, I will purge the mito sequences and assemble the genome
8. Run miranda with lncRNAs - yes
9. Run DEG analysis with lncRNAs - yes

Pretty good month! I got a lot of data analysis done (motivated by the temperate coral conference).