October 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. e5 ncRNA complete draft of manuscript
2. Pacuta manuscript send to coauthors for edits
3. AST results for manuscript

Sample processing

1. Send WGBS e5 deep dive samples
2. Phys stuff for AST and Mcap DT ?

Data analysis

1. Make fasta for 3’UTRs with gene names and rerun miranda
2. Run mirtarrnaseq for AST and make figures for manuscript
3. Run mirtarrnaseq for deep dive (Apul) - need count matrices for both miRNA and mRNA and miranda info
4. Figure out trimming for miRNA data Mcap DT 2023
5. Compiling all phys stuff for AST 2021 (if time)

Field work / travel

1. Resgister for sicb
2. Book flights for sicb
3. Confirm travel for cbass workshop

Daily log

20241101

• e5 ncRNA paper writing
• e5 meeting
• Running miranda for updated miRNAs e5

20241103

• Playing around w mirtarrnaseq

20241104

• mirtarrnaseq Apul e5 deep dive expression
• Mote interview
• Lab meeting
• Prospective student meeting
• Aquarium room stuff

20241105

• Cutadapt iterations for DT samples
• Writing for e5 ncRNA manuscript
• Sent e5 draft to authors

20241106

• bleh
• Writing accountability
• Sent Pacuta manuscript to authors
• Changed water for larvs
• beach screm

20241107

• Writing meeting
• Aquarium room stuff
• Hollie meeting
• Looking at multiQC
• Shortstack coding

20241108

• Despairing over smRNA dups
• Writing accountability
• Edits to Pacuta paper
• lncRNA Mcap identification
• Danielle practice defense

20241110

• Small edits for Pacuta paper

20241112

• Small edits for Pacuta paper
• Moved settled Pacuta into blue tank 1/2
• Ran shortstack on the samples from seq batch 1
• Downloaded rfam seqs
• Blasting putative mcap lncRNAs against rfam db
• mirdeep2 mapper for mcap dt 2023

20241113

• mirdeep2 mirna prediction for mcap dt 2023
• Started sicb presentation
• Kallisto and trinity for mcap lncRNAs
• Lab meeting
• Zach meeting
• DESeq2 for mRNA and lncRNA mcap data
• lncRNA - mRNA co-expression analysis

20241114

• Fixing shortstack headers for AST miRNAs
• Writing meeting
• Set up larval system in aquarium room

20241115

DANIELLE DEFENSE!!!!!!!!!!!!!

20241117

• Cassie practice defense

20241118

• AST mirtarrnaseq
• Prep for e5 sample processing
• RIblast db creation for mcap
• Reran mapper.pl for AST

20241119

• Dentist
• RIblast RNA interactions for mcap
• Started to rerun mirdeep2.pl for AST
• Protein plate for e5 test samples
• Protein calculations for e5 test samples
• Searching for e5 samples

20241120

• Drop car off
• President visit
• Found rest of e5 samples
• Edits to Pacuta paper
• Bioinformatic methods for Mcap DT (mRNA and lncRNAs)
• mRNA lncRNA co-expression for mcap - will need to run on unity
• CASSIE DEFENSE!!!!!!!!!!!!!!!

20241121

• Zoe practice oral exam questions
• Continuing to explore mRNA lncRNA co-expression for mcap
• Looked at mirdeep2 AST output
• Looked at cutadapt results for smRNA mcap