February 2025 goals and daily notebook entries.

Goals

Writing and manuscripts

1. e5 ncRNA complete draft of manuscript submit to biorxiv (chapter 1)
2. Astrangia 2021 results and discussion (chapter 2)
   • Linking miRNA mRNA regulation and pathways
   • Discussing positive and negative miRNA correlations
3. Complete my section CBASS results + discussion

Sample processing

1. Switchfree library prep for Mcap 2023 samples
2. Protein assay for 96 lipid/metabolite e5 samples

Data analysis

1. e5 deep dive expression
   • Name updated miRNAs for 3 species
   • Summarize number of targets of each miRNA, positive/negative correlations, etc
   • Compare/contrast miRNA function with previous lit
2. Astrangia 2021 continue analysis for miRNA mRNA interactions (chapter 2)
   • Pathways of interest for discussion
   • Plot number of binding sites by energy score - done 2/2/25
   • Spearman rank correlation in addition to Pearson’s (Zhang et al. 2018)
3. Mcap miRNA trimming and identification (chapter 2)
4. DE analysis for Mcap miRNA and mRNA data (chapter 2)
5. CBASS plots and tables
   • Make nice figures for paper
   • Make stats supplementary tables

Field work / travel

1. Fill out TERs (CBASS and sicb)

Daily log

20250201

• Switchfree library prep w/ Mcap 2023 samples

20250202

• Switchfree library prep w/ Mcap 2023 samples

20250203

• AST writing (chapter 1)
• Lab meeting

20250204

• AST writing (chapter 1) + functional enrichment coding

20250205

• Switchfree library prep w/ Mcap 2023 samples
• e5 deep dive expression coding
• Some AST writing (chapter 1)

20250206

• Submitted pacbio bam to SRA
• e5 deep dive expression coding and writing
• TER for sicb

20250207

• e5 deep dive expression coding and writing
• Trinity talk
• Colloquium

20250209

• e5 deep dive expression coding and writing

20250210

• Lab meeting
• AST writing (chapter 1)
• Organizing AST repo to some degree
• Attempted to rename miRNAs for e5
• Requested genohub quote for mcap libraries (request 8599420)
• Run mirdeep2 quant for Mcap 2023 - boo
• Despairing over my lack of organization with AST 2021 phys

20250211

• AST writing (chapter 1)
• Chloe meetup

20250212

• Writing time - writing potential questions
• Getting rid of unneeded files on Andromeda
• Looking into ways to deal with my Mcap smRNA data
• Nia meeting

20250213

• Writing time
• Mcap 2023 coding smRNA
• e5 coding - miranda with miRNAs and mrna/transcripts
• Resubmitted SICB TER
• Hollie meeting
• Made draft committee meeting presentation

20250214

• Submitted cbass TER
• DT 2023 mcap coding and writing
• e5 meeting
• Astrangia writing
• Worked on committee presentation

20250216

• Reviewer for RSO - complete

20250217

• Lab meeting
• Renamed miRNAs for e5 deep dive expression
• AST 2021 figure making
• Trimming for Mcap 2023 smRNA

20250218

• Trimming for Mcap 2023 smRNA
• biomin blast for AST, POC, POR
• Blasting mir100 against raw collapsed reads for M9 (first batch) and M6 (second batch)
• Trimming first batch (n=8) with updated flexbar parameters

20250219

• Ran mapper.pl on flexbar first batch 35 and 75bp
• Ran short stack with flexbar first batch 35 and 75bp - i think it got confused
• Aligned M6 50bp with bwa and looked at alignment stats w samtools
• Started mirdeep2.pl run with flexbar first batch 35bp
• topGO for modules
• Trimming stuff
• Rerunning first batch of samples through mirdeep2 pipeline
• Running all trimmed flexbar samples to 30bp through mirdeep2 pipeline
• wgcna for lncRNAs

20250220

• NYUAD interview
• Writing meeting
• Writing e5 ncrna and AST 2021

Notes

• GSA for maldives