June 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Submit molecular underpinnings (Ch.1)
2. A.pul gametogenesis final figures, results sections for histology analysis
3. Marine heatwaves manuscript transcriptome and gene expression

Sample processing

1. Histological image analysis (abundance and size)
2. Library prep for heatwave WGBS samples (12)?

Data analysis

1. Work on DEG analysis for heatwave after mapping sequences to de novo transcriptome
2. Histological image/gonad analyses
3. Finish biomass data for gametogenesis

Daily log

June 3

• Hollie meeting
• Restructured Ch1 geneious alignment
• Finished phys results section Ch3
• Entered in heatwave biomass data
• Kelp timeseries analysis and manuscript figures generation

June 4

• Titration training for undergraduates
• Heatwave biomass for sym and host analysis and figures generation
• Kelp timeseries analysis and manuscript figures generation

June 5

• Ch1 comparisons from functional, structural, and gff3 files
• Histological analysis
• Kelp timeseries analysis and manuscript figures generation

June 6

• Histological analysis
• Kelp timeseries analysis and manuscript figures generation
• Code for statistical post-hoc letters for figures in results section Ch3

June 7

• Histological analysis
• Ch3 post-hoc stats to phys figures
• Austin kelp timeseries meeting
• Ch1 amended workflow updates for issue #4 in Becker_E5 repo

June 10

• Off in NYC

June 11

• Histology analysis
• Austin summer hours kelp timeseries data analysis
• Started workflow for modified and fixed gff3 comparison on andromeda
• Updated ch3 code to include post-hoc data

June 12

• Histology analysis
• Austin summer hours kelp timeseries data analysis
• Finished workflow for modified and fixed gff3 comparison on andromeda
• Updated prepDE.py3 python code for stringtie

June 13

• Histology analysis
• Austin summer hours kelp timeseries data analysis
• Created projects in IGB for looking at gene counts for modified and original gff3 files

June 14

• Finished spermatogenesis and oogenesis photo data analysis through September in ImageJ/FIJI
• Ran stranded and nonstranded references transcriptomes in blast to compare outputs for next steps

June 17

• Kelp timeseries model restruture
• Updated kelp timeseries manuscript figures 1-7
• Austin meeting
• Histology analysis through October
• Ch1 issue for .gff3, looked at modified and original in IGB, all checks out visually

June 18

• Ariana meeting
• Updated Ch1 goseq code and analysis with new filtering and background dataset approach
• Updated Ch1 methods and results sections
• Ch3 results sections and Ch2 hypotheses update

June 19

• Off for Juneteenth

June 20

• Ch2 histology analysis through October, need to look at three samples on hard drive then finished!
• Hollie meeting
• Meeting summary and agenda updates
• Apex troubleshooting in wetlab
• Ch1 literature review and troubleshooting goseq script and analysis

June 21

• Ch1 issue for .gff3, looked at modified and original in IGB, all checks out visually
• Kelp timeseries updated data analysis and made proportional kelp change per year code and plot
• Started looking into and prepping workflow for contaminant filtering from Ch3 reference transcriptomes

June 24

• Ch1 goseq issues on different modules and versions, Ariana and I worked on troubleshooting this for a while
• Kelp timeseries data analyses and figures
• Ch2 finished October samples, all complete!
• Aquarium room duties, apex troubleshooting

June 25

• Knauss notification!!!!
• Some light computer work for Kelp timeseries manuscript

June 26

• Ch2 updated gameto timeseries code and final figures
• Aquarium room duties, apex troubleshooting

June 27

• Look into contaminant and symbiont filtering for reference transcriptomes on Jill and Ross’s codes and workflows, began writing scripts for next steps
• Austin meeting and working through Kelp timeseries manuscript and figures
• Aquarium room duties, submitted work orders for Apex products that need to be replaced or sent in
• Some packing and organizing for Sarah and Flo for Bermuda, got items from GSO
• Completed Sarahs TAR for Bermuda

June 28

• Aquarium room duties, Apex connection issues, some resolved
• Completed Elizas TAR for Bermuda
• Some packing and organizing for Sarah and Flo for Bermuda