July 2024 Goals

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

Data analysis

  1. Work on DEG analysis for heatwave
  2. Finish biomass data entry for Ch2
  3. Correlation analyses and variance partitioning/redundancy analyses for Ch2

Daily log

July 1

  • Out for NYC travel
  • Aquarium duties and cleaning

July 2

  • Aquarium duties and cleaning
  • Completed filtering for euk, prot, and viral contaminants for stranded and nonstranded reference transcriptomes
  • Running symbiont filtering script on stranded and nonstranded reference transcriptomes
  • Kelp timeseries work

July 3

  • Ran viral, prot, and euk contam filtering on stranded and nonstranded references
  • Kelp timeseries TA work
  • Ch2 finished histology analysis!
  • Ch2 univariate organization and analysis

July 4

  • Off for holiday

July 5

  • Kelp timeseries TA work
  • Worked on script for contaminant filtering for Ch3
  • Ch3 results section updates
  • Submitted Ch1 goseq concerns to Bioconductor working group

July 8

  • Kelp timeseries TA work
  • Completed script for contaminant filtering for Ch3
  • Wrote script and submitted job to filter contaminants from stranded and nonstranded references, ran into errors but trying new script
  • Fellowship informational meeting
  • Fielded Ch1 goseq concerns on Bioconductor working group

July 9

  • Fellowship headshots at GSO
  • Ch2 univariate analysis work
  • Kelp timeseries TA work

July 10

  • Ch2 univariate analysis work
  • Kelp timeseries TA work
  • Putnam lab meeting, discussed goseq and functional enrichment issues for Ch1

July 11

  • Aquarium duties, titrations, salt mixing, dose adjustments
  • Ch2 univariate analysis work
  • Kelp timeseries TA work
  • Literature review for multivariate analyses for Ch2
  • Helped Eliza find materials and prep for Bermuda

July 12

  • Aquarium duties, titrations, salt mixing, dose adjustments
  • Ch2 univariate analysis work
  • Kelp timeseries TA work
  • Literature review for multivariate analyses for Ch2

July 15

  • Aquarium duties, added DI to header
  • Fellowship meeting and form submission
  • Kelp timeseries TA work
  • Ch3 script completed running for making contam free fasta, cross checked filtering process and resubmitted script

July 16

  • Aquarium troubleshooting with Neptune support for power issues in system, sending new EB832 for us for free due to voltage issues
  • Kelp timeseries TA work
  • Ch3 de novo transcriptome updates to methods and results sections
  • Ch2 continuing working on updating univariate physio figures with sig letters on each plot

July 17

  • Ch2 updated sig letters on plots, updated methods and results sections
  • Ch3 updated transcriptome methods and results sections
  • Ran Ch3 trancriptome filtering of contam transcripts code after troubleshooting on andromeda
  • Austin TA meeting and TA work

July 18

  • Ch2 finishing data entry for sym and host biomass, update phys results sections
  • Ch3 transcriptome filtering end .fasta not matching contam filtering .txt file, looking intoscript issues
  • Submitted Sarahs TER
  • Fellowship office hours meeting
  • Kelp timeseries TA work

July 19

  • Fellowship meetings
  • Updated Ch3 transcriptome filtering script, re-ran to try and solve filtering error
  • Continued data entry for Ch2 biomass for months April-October
  • Literature review of multivariate stat approaches for Ch2
  • Kelp timeseries TA work

### July 22

  • Diving for kelp TA work requirements
  • Ran biomass data for all Ch2 and updated phys and sym plots with letters for sig
  • Concatenated transcripts from nonstranded and stranded assemblies

### July 23

  • Diving for kelp TA work requirements
  • Updated multivariate analyses for correlation plots and PCA for ch2
  • Literature review for ch2 analysis

### July 24

  • Kelp TA timeseries analysis and data entry
  • Putnam lab meeting
  • Updated multivariate analyses for correlation plots and PCA for ch2
  • Re-ran busco for final transcriptome assembly

### July 25

  • Kelp TA timeseries analysis and data entry
  • Updated combined assembly for reference transcriptome, running into errors with duplicates when concatenating assemblies
  • Fellowship meetings
  • Started reanalyzing Ch1 enrichment data with goMWU scripts and approach
  • Multivariate analysis work for Ch2

### July 26

  • Kelp TA timeseries analysis and data entry
  • E5 meeting
  • Fellowship meetings
  • Updated combined assembly for reference transcriptome
  • Ran BP for goMWU for ch1 on andromeda
  • Ch2 literature review for multivariate approaches

### July 29

  • No results for goMWU, ran topGO for DEGs and updated molecular underpinnings manuscript
  • Wrote scripts and started workflow for ch3 transcriptome cd-hit-est
  • Updated ch2 staging guide and results sections
  • Wrote out hypotheses in each chapter for Hollie

July 30

  • Kelp TA timeseries analysis and data entry
  • Aquarium duties
  • Ran topGO for DEGs and updated molecular underpinnings manuscript
  • Wrote out hypotheses in each chapter for Hollie
  • Methods and results for updated transcriptome

July 31

  • Titrations and aquarium duties
  • Kelp TA timeseries analysis and data entry
  • Ran topGO for DMGs and updated molecular underpinnings manuscript
  • Methods and results for updated transcriptome
  • Make workflow for cd-hit-est and updated mapping to genome for ch3
Written on July 1, 2024