August 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Submit molecular underpinnings (Ch.1) to BioRXiv by end of month
2. A.pul gametogenesis multivariate analysis
3. Marine heatwaves manuscript transcriptome and gene expression

Sample processing

1. Library prep for heatwave WGBS samples (12)?

Data analysis

1. Work on DEG analysis for heatwave
2. Variance partitioning/redundancy analyses and condition indices for Ch2
3. Ch3 gene expression

Daily log

August 1

• Updated methods and results for transcriptome, ran cd-hit-est for transcriptome
• Updated results and methods for ch2
• Updated DEG and DMG results and discussion sections for Ch1 from topGO

August 2

• Redid topGO for DEGs with Hollie suggestions
• Responded and addressed Hollies edits and comments on methods and results sections for Ch1
• New approach for topGO

August 3

• Redid topGO for DEGs with Hollie suggestions
• Responded and addressed Hollies edits and comments on methods and results sections for Ch1
• New approach for topGO for ch1, updated results sections and made tables for top DEGs

August 5

• Ch1 genes of interest list compilation
• Confirmed defense date and time with committee members
• Ch3 transcriptome mapping workflow, functional annotation workflow
• Updated hypothesis and edits for ch2 and ch3
• New approach for topGO for ch1, updated results sections and made tables for top DEGs

August 6

• Ch1 genes of interest list compilation and literature review
• Ch3 transcriptome mapping workflow to updated A.pul genome, functional annotation workflow and literature review for Trinotate approach
• Updated hypothesis and edits for ch2 and ch3

August 7

• Aquarium duties, adjusted alkalinity outputs
• Ch1 genes of interest list compilation and literature review
• Slide scanning at Brown for new POC samples
• Kelp timeseries manuscript and MERMAID data entry
• Aligned reads to de novo transcriptome for ch3, running RSEM for all samples

August 8

• Aquarium duties
• Ch1 genes of interest list compilation and literature review
• Kelp timeseries manuscript and MERMAID data entry
• Continued workflow for running RSEM for samples, CH3
• Updated correlation figures for DEG and DMG for CH1
• Rewrote results sections for Ch1 for DEG topGO
• Rerunning BS-SNPer with only 29 samples instead of 32

August 9

• Ch1 genes of interest list compilation and literature review
• Literature review for Ch3 transcriptome functional annotation, began workflow on Andromeda for trinotate
• Reworked ch2 hypotheses with literature based approaches for more targeted approach than overarching correlations across all timepoints
• Rerunning BS-SNPer with only 29 samples instead of 32

August 10

• Comments and review of CEABiGR Manuscript for requested re-submission of revisions

August 11

• Comments and review of CEABiGR Manuscript for requested re-submission of revisions

August 12

• Ch1 genes of interest list compilation completion
• Literature review for Ch3 transcriptome functional annotation, continued working on workflow on Andromeda for trinotate
• Reworked ch2 hypotheses with literature based approaches for more targeted approach than overarching correlations across all timepoints
• Rerunning BS-SNPer with only 29 samples instead of 32

August 13

• Ch1 correlation plots, DEG, DMG comparisons
• topGO for DMGs and genes of interest compilation
• Literature review for Ch3 transcriptome functional annotation, continued working on workflow on Andromeda for trinotate
• Reworked ch2 hypotheses with literature based approaches for more targeted approach than overarching correlations across all timepoints

August 14

• COVID rest day

August 15

• Ch1 correlation plots, DEG, DMG comparisons
• topGO for DMGs and genes of interest compilation
• Literature review for Ch3 transcriptome functional annotation, continued working on workflow on Andromeda for trinotate
• Reworked ch2 hypotheses with literature based approaches for more targeted approach than overarching correlations across all timepoints
• Ch2 updated introduction final paragraph

August 16

• Ch1 updated results and discussion paragraphs with new data and filtering step
• Ch2 wrote size and relative abundance results sections, updated introduction paragraphs
• Ch2 updated size and relative abundance figures, made stacked timeseries plot with data
• Ch3 noticed alignment rates through RSEM and bowtie2 lower than Hisat2, looking into literature and code

August 17

Continued working on:

• Ch1 updated results and discussion paragraphs with new data and filtering step
• Ch2 wrote size and relative abundance results sections, updated introduction paragraphs
• NSF annual report
• Ch3 HISAT2 and stringtie workflow

August 18

Continued working on:

• Ch1 updated results and discussion paragraphs with new data and filtering step
• NSF annual report
• Ch3 HISAT2 and stringtie workflow

August 19

• Ch1 updated results and discussion paragraphs with new data and filtering step
• Ch3 HISAT2 and stringtie workflow
• NSF annual report

August 20

Continued working on:

• Ch1 updated results and discussion paragraphs with new data and filtering step
• NSF annual report
• Ch3 stringtie and assembly

August 21

Continued working on:

• Ch1 updated results and discussion paragraphs with new data and filtering step
• NSF annual report
• Ch3 stringtie workflow
• Ch2 updated size figures for NSF report

August 22

• Finished stringtie and updates for transdecoder workflow, got gene count matrix
• DEGs for adult heatwave
• Aquarium duties

August 23

• DEGs for larval parental history
• Ch1 reviews to Emma
• Ch3 heatwave results sections

August 26

• Ch1 edits and submission to Hollie
• Aquarium duties

August 27

• Updates to NSF annual report for Ch2 and Ch3
• Updated Ch2 figures and tables
• Updated Ch3 figures and tables
• Slide processing at Brown

August 28

• Slide processing at Brown
• Ch3 methods and results for DEGs
• Ch3 DEG figures finalized, script updates

August 29

• Hollie meeting
• Ch2 relative abundance analysis
• Ch1 edits and updates

August 30

• Ch1 edits and updates
• Ch3 functional annotation
• Ch3 DEG results and methods sections