April 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. Finish intro and methods for e5 ncRNA paper
5. Methods + results for Pacuta paper

Sample processing

1. Extractions + 3’ mRNA library prep with POC samples
2. Library prep for WGBS (27 samples)
3. Carbs for DT samples

Data analysis

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

Daily log

20240401

• Looked at busco output for s30 assembly
• Started running busco for s80 assembly
• Blast of mito seqs against Apul pacbio raw reads
• Plotting + figuring out DT Mcap 2023 mRNA expression data (LPEseq since no replicates)
• LPEseq w/ Mcap 2023 data
• Caroline defense
• Labeling tubes for extractions and library prep
• Moving stuff in lab for electric guy tomorrow
• DT Mcap 2023 smRNA samples back from sequencer!
• Registered for temperate coral conference
• Busco results for s80
• quast for all assemblies so far

20240402

• Met w/ Madeline re swms
• Lab meeting
• Pacuta results section
• Aquarium room
• Therapy
• Taxes

20240403

• Extractions + QC w/ 6 POC samples
• Updating notebook db + posts
• Lab meeting
• Hollie meeting
• Looking at DT Mcap 2023 PCA + making plans for future lib prep + sequencing

20240404

• Sections 1 and 2 of 3’ mRNA library prep with POC samples
• DMV
• Collecting e5 ncRNA protein machinery info

20240405

• Section 3 of 3’ mRNA library prep with POC samples + QC
• e5 molecular mechanism meeting
• Collecting e5 ncRNA protein machinery info
• Juliane defense
• Genohub quote

20240407

• Worked on Astrangia review, need to cut words

20240408

• Letter to editor for Biology Letters
• Editing/cutting words in Astrangia review
• Remade some figures for Pacuta 2022 manuscript
• Diagrams of workflows for each chapter
• Genohub submission sheet for 12 POC samples, send tomorrow
• Trying to install mito hifi
• Wrote methods for Pverr paper

20240409

• Shipped POC samples for sequencing
• Shipped Pacuta to Katie
• Code w/ Chloe
• Writing meeting
• 3’UTR seq coding
• Therapy
• Astrangia review letter to editor

20240410

• 3’UTR DEG extraction
• Meeting w/ Olga
• Talked w/ Zoe
• Started miranda run with differentially expressed miRNAs and genes

20240411

• Miranda run with -strict flag
• Looking at miranda output
• Gathering ncRNA fasta prot info on HPC
• Blasting ncRNA proteins against e5 deep dive spp proteins
• Sent review proposal to biology letters
• Starting bios app

20240414

• miRNA:mRNA functional enrichment analysis
• Working on astrangia abstract for conference

20240415

• Moved AST 2021 histology samples into 2ml tubes w/ Chloe
• Rec letter + statement for BIOS course app

20240416

• Moved rest of histo samples w/ Chloe
• Hollie meeting
• Lab meeting
• Therapy
• Coding co-expression plots for mRNA:miRNA (only looking at TP0vTP5 amb)
• BIOS rec letter
• Edits to Chloe abstract
• Updated histo inventory

20240417

• ITS2 trial + QC
• Lab meeting
• Talked w/ Zoe about co-expression analyses
• Finished BIOS letter of rec
• Closed genohub smRNA-seq project

20240418

• Rest of ITS2 samples + QC
• Aquarium room stuff
• Glued fingers to glue bottle
• Finished Astrangia abstract for Temperate coral conference

20240419

• Lulu defense
• Downloaded ncRNA e5 prot info onto github
• Worked on responses to biology letter review questions
• Sent Ariana BIOS letter of rec
• Playing w/ multiple sequence alignments for ncRNA prots
• e5 meeting
• meeting w/ chloe

20240420

• Submitted Astrangia abstract for temperate coral conference

20240421

• mRNA and miRNA DEGs AST 2021
• Started WGCNA for mRNAs AST 2021
• Started miranda run with all mRNA and miRNAs
• Quantified AST 2021 lncRNA transcripts into count matrix
• lncRNA AST 2021 Deseq2 analysis

20240422

• GRFP fellow update, sent to Hollie for signature
• Started miranda run with all lncRNAs and miRNAs–failed
• Tried to get mirTarRnaSeq to work with my data
• Going through vignette mirTarRnaSeq example data

20240423

• Aquarium room duties
• Writing meeting
• Editing bios course statement
• Submitted GRFP report + declared fellowship status for next year
• Therapy
• Histology clean up
• ICRS indigenous and local scientists workshop
• Finished BIOS statement

20240424

• Edited AH BIOS letter of rec
• Writing results for Pacuta 2022 paper
• POC seqs back from sequencer!

20240426

• Restarted miranda runs
• Writing go slim results for Pacuta 2022 paper

20240429

• Made BIOS CV
• Writing about data analysis for dissertation proposal

20240430

• Submitted BIOS app
• Lab meeting
• Therapy
• Working on GO figures for Pacuta 2022 manuscript

April reflection

How did I do with my goals for this month?

Writing and manuscripts

1. Full draft of dissertation proposal - nope but should have it finished this Friday (5/3)
2. Write physiological results for Astrangia 2021 experiment - nope. Need to go through lab notebooks to make sure I got all phys samples processed
3. Resubmit Astrangia review manuscript - nope. Need to send editor the questions about why the manuscript is relevant to Biology Letters
4. Finish intro and methods for e5 ncRNA paper - kinda? waiting on some methods from Sam White
5. Methods + results for Pacuta paper - Yes!

Sample processing

1. Extractions + 3’ mRNA library prep with POC samples - Yes! Received data back & Hollie is currently processesing
2. Library prep for WGBS (27 samples) - nope
3. Carbs for DT samples - nope

Data analysis

1. Finish stats for Astrangia 2021 phys data (carbs) - nope, need to go through lab notebooks to make sure I got all phys samples processed
2. Complete Astrangia 2021 mRNA functional enrichment analysis - Yes!
3. Run miranda with genes of interest, invoking strict seed binding - yes, currently running on the server
4. Assemble mito genome for Apul - nope but should be getting MitoHiFi up and running this week
5. Assemble coral genome for Apul - nope, but once I assemble the mito genome, I will purge the mito sequences and assemble the genome
6. Run miranda with lncRNAs - currently running on the server
7. Run DEG analysis with lncRNAs - yes! Need to check poverA filtering