Kaitlyn’s notebook: O. lurida dissections and measuring geoduck


I spent some time going through the measurements made during dissection to ensure everything was correct. There were quite a few errors or over sites that needed fixing so I’m glad I took the time to do this.Everything is finalized in the spreadsheet now (linked in my previous two posts). I highlighted any inaccuracies, missing measurements or incomplete recordings.

I also wanted to make a note here of who did what one each day of the dissections:

9/6/18: Fidalgo Bay- Duncan cleaned and measured oysters while I recorded measurements he called. Emily and Micah did large pouches and dissections.

9/7/18: Case Inlet- Emily and Micah separated pouches and were about halfway through measurements and dissections when I arrived and measured and recorded small oyster bags.

9/8/18: Port Gamble- Emily and Micah did the large pouches and dissections while I did the small pouches. Corey and Eliza arrived to help but we were mostly done. They helped measure and record a few bags though!

9/9/18: Skokomish- It was just Emily, Micah and I today. They did large bags and dissections while I did small bags again.

All dissections were done in 213 and tissue samples were flash frozen in liquid nitrogen before being out in the -80C. Digital calipers were used the first two days and the last two days both digital and an analog caliper was used. The scale in 209 was used for mass.

Pouch/length datasheet:


Tissue sampling datasheets:


Geoduck Measurements

I’m starting to measure the geoduck from outplanting. One horizontal line on the grid is 18mm long. I use this for the set measurement. However, each group will need this redone because the distance and zoom between images is variable.

I just started measurements, but I am saving ROI sets as I did with previous ImageJ measurements I’ve done.

Sam’s Notebook: DNA Quantification – Sea Lice DNA from 20180523


We previously received sea lice (Caligus tape) DNA from Cris Gallardo-Escarate at Universidad de Concepción.

Steven asked that I quantify and assess the DNA quality.

Ran the samples on the Roberts Lab Qubit 3.0 using the dsDNA BR assay (Invitrogen) and 1uL of template DNA.

Ran the samples on the Roberts Lab NanoDrop1000 to get 260/280 values for quality assessment using 2uL of template DNA. NanoDrop1000 was blanked with water, but I don’t know what solvent the DNA is currently resuspended in.

Kaitlyn’s notebook: Skokomish dissections

The final day of dissections! Survival was not nearly as low as Fidalgo Bay, and extra organism (worms/Polydora, etc.) burden was comparable to that of yesterday. Dissections went well and I cleaned up the lab afterwards. Micah left Laura;s oyster nets here underneath the lab bench in 213. I wasn’t sure of a better spot to put them since they are so big. All of the whole body and gut/gill samples are in the -80 next to Ronit’s samples. I’m hoping to clear out a spot for them this upcoming week. (I also labelled and consolidated Ronit’s samples.)

I also mostly finished entering the data– it just needs to be rechecked for errors. I’ll post backup images of the hard copy datasheets once I finish double checking the google spreadsheet.

Yaamini’s Notebook: DML Analysis Part 8

DML-mRNA Gene Enrichment Results

Yesterday, I went through DML-mRNA overlap gene enrichment in DAVID (see my lab notebook post), but I was unable to generate plots in ReVIGO. Turns out my issue with ReVIGO was related to Adobe Flash. Once I updated my flash player, I was able to create the interactive graphics. I added the graphics and explanations below to my R Markdown file as well. I probably need to learn how to use the R script to generate plots for reproducibility purposes, but that can wait.

I pasted significant GOterms and p-values into ReViGO to generate the following figures. For each category, I created a plot with medium term similarity, and either sizes based on logSize or log10p-value.

Biological processes:

Processes include cytoskeleton and microtubule movement, cell cycle, and protein activity. The most interesting results were those related to DNA and reproduction. DNA replication, mRNA processing, positive regulation of transcription from RNA polymerase II promoters, and response to DNA damage were all enriched. Additionally, enrichment positive regulation of histone H3-K9 acetylation, methylation-dependent chromatin silencing, DNA methylation involved in gamete generation, and fertilization point to mechanisms for epigenetic inheritance! This is going to be the central finding of my PCSGA talk.



Cellular components:

Cellular components involved in enriched processes included protein complexes, transcription factor complexes, chromosomes, centromeres, microtubules, and cilia.



Molecular function:

Molecular functions of enriched processes include GTPase and ATPase activity, helicase activity, microtuble motor activity, protein kinase binding and activity, transcription regulatory region DNA binding, general DNA binding, and ion binding.



It’ll be interesting to see how the DAVID gene enrichment compares to the Mike Riffle’s gene enrichment tool, or how gene enrichment in the other components will complicate the story. For now, I have enough to work with for PCSGA.

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