September 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Dissertation proposal submission to grad school
2. IDP + plan outline
3. Post doc fellowship apps
4. e5 ncRNA complete draft
5. Pacuta manuscript submission

Sample processing

1. Re-amp 6 WGBS e5 deep dive samples
2. Phys stuff for AST and Mcap DT
3. Find and send DNA for e5 samples
4. Metabolomics test samples for e5 time series

Data analysis

1. 3’UTR for AST 2021 (GENE EXT) and rerun miRanda with that info
2. Apul methylation w/ pacbio tools
3. Compiling all phys stuff for AST 2021

Field work / travel

1. Figure out travel for cbass workshop
2. Apply for travel $$$ for cbass workshop
3. Apply for travel $$$ for sicb

Daily log

20240901

• Installing gene ext again, failed
• Writing some NSF PRFB ideas
• Apul genome methylation initial analysis
• DESeq2 with shortstack miRNA output
• Started UNCW cover letter

20240902

• Separations for metabolomics samples
• Edits to Pacuta 2022 intro
• UNCW cover letter
• Mote cover letter
• Created shipping label for test metabolomics samples tomorrow

20240903

• Shipped test metabolomics samples
• New grad student tour
• Shipped corals
• Talked w Zoe re cover letters
• BES retreat

20240904

• Resubmitted Bermuda TER
• Looking over e5 timeseries RNA QC
• Closed some deep dive e5 github issues
• Updated EHS refresher training
• Finished UNCW cover letter

20240905

• Picked up science saturday shirts
• Random science saturday stuff
• Nanodropped DNA samples and WGBS libraries
• Wrote up nanodrop post
• Submitted UNCW app!!!!!!
• Worked on JEB travel app

20240906

• submitted time sheet
• JEB travel app
• e5 meeting
• piRNA closest
• steven meeting

20240907

• Science saturday

20240908

• Metabolomics separations + shipping prep
• A few edits to Pacuta paper intro
• JEB travel app

20240909

• Shipped metabolomics samples
• Lab meeting
• Organizing go stuff for ncRNA closest gene
• Storage inventory

20240910

• Trinity meeting
  • Location of soft-masked genome: /data/putnamlab/tconn/repeats/apul_softmasked/apul.hifiasm.s55_pa.p_ctg.fa.k32.w100.z1000.ntLink.5rounds.fa.masked
• Looking into pacbio methylation analysis
• Writing for apul genome paper
• Sent JEB info to Hollie
• GO enrichment code
• Therapy
• Booked maldives flights

20240911

• Writing accountability - dissertation proposal + sent to Hollie
• GO enrichment for genes closest to ncRNAs in genomes e5 - made plots, updated manuscript

20240912

• Go enrichment figures + writing
• lncRNA bed closest + go enrichment + figures
• Attempted to run gene ext in Zoe’s directory, failed
• Results writing for e5 ncRNA paper
• Cleaning up methods + intro for e5 ncRNA paper

20240913

• IDP writing
• e5 ncRNA writing
• Remaking plots for e5 ncRNA
• posts for reefbites
• Talking w/ Danielle re her last chapter

20240915

• e5 writing
• IDP
• Coding for acute thermal stress HI 2022
• Mote cover letter

20240916

• JEB app
• Looking at e5 molecular sample stuff
• Genohub w/ Zoe
• SICB travel w/ Zoe
• Lab meeting

20240917

• Mote app
• Finished uploading assembled genome to NCBI
• Therapy
• e5 ncRNA paper writing
• Titration for QT
• Updating e5 ncRNA fig 1

20240918

• Writing accountability - e5 ncRNA discussion
• Pacuta paper cleaning up results section
• Tried to run jasmine on raw hifi reads, failed
• Made table for Pacuta paper
• JEB app
• Helping with various lab things

20240919

• Writing meeting
• Pacuta paper intro
• PACUTA LARVAE!!!!!
• NSF PRFB webinar
• DT MCAP seq data received!!!
• QCed Mcap seq data
• Jackie meeting

20240920

• Looking at e5 ncRNA stuff
• DIBP
• e5 meeting
• Worked on e5 ncRNA paper
• Changed water out for larvae in plates 1+2 and added substrate for larvae in plates 3+4
• Colloquium

20240921

• Water change for larvae

20240922

• Water change for larvae

20240923

• Re-Qubit for e5 DNA
• Aquarium room stuff
• Looking at e5 DNA timeseries stuff
• Lab meeting
• Remaking e5 figs

20240924

• Remaking e5 figs
• Emails + admin stuff
• Submitted Mote app
• Looking at PacBio methylation info + downloading bunch of pb tools to andromeda
• Aligning pacbio bam to reference for meth analysis

20240925

• DNA extractions for e5
• Water change for larvae
• Read Chloe GRFP app
• Looking at cpg-tools output for Apul

20240926

• QC DNA
• Methods and results for Apul methylation
• Notebook post for extractions
• PacBio methylation meeting
• QC mcap data

20240930

• Aquarium room stuff
• Lab meeting
• Looked at Mcap QC
• Prep for e5 writing retreat
• Apul methylation + gene intersect
• Outline for lab meeting next week

September reflection

How did I do with my goals for this month?

Writing and manuscripts

1. Dissertation proposal submission to grad school - nope, on Hollie’s desk
2. IDP + plan outline - yes kinda. No plan outline but have some rough dates
3. Post doc fellowship apps - no lol. Probably wont apply this cycle because I am overwhelmed
4. e5 ncRNA complete draft - kinda? Basically there
5. Pacuta manuscript submission - nope but getting close

Data analysis

1. 3’UTR for AST 2021 (GENE EXT) and rerun miRanda with that info - nope. tried to install but lots of fails. May just have zoe run it
2. Apul methylation w/ pacbio tools - yes!!!
3. Compiling all phys stuff for AST 2021 - nope

Sample processing

1. Re-amp 6 WGBS e5 deep dive samples - kinda. I have done some troubleshooting but will figure out how to move forward next week
2. Phys stuff for AST and Mcap DT - nope
3. Find and send DNA for e5 samples - kinda? Did some re-extractions on POR samples, now need to decide how to move forward
4. Metabolomics test samples for e5 time series - yes

Field work / travel

1. Figure out travel for cbass workshop - yes, flights booked
2. Apply for travel $$$ for cbass workshop - application in the works
3. Apply for travel $$$ for sicb - yes

I got a lot of writing done this month! Several manuscripts are close to submission. I’m also happy that the methylation for the Apul genome is complete.