Sean’s Notebook: Water Samples at DNR in Olympia


After many trials and tribulations, I’ve finally started running real honest to god TA samples from Hollie’s geoduck experiment. It took a few CRM runs for the new probe on the titratior to settle down, but I got three reps within 10 TA units of each other (They were reading ~20 units higher than expected, so I’ll likely just use an offset to account for that). Progress!

Now only a few hundred more samples to go…

On the Hyak front, after finishing Andrew’s salmon run, I’ve started running the platanus assembler on the Oly Illumina data. After Platanus finishes, we’ll try to integrate the long read PacBio stuff via Redundans. Hopefully PBJelly will finish the gap filling process so we will have two assemblies to compare.

Kaitlyn’s Notebook: Silo 2 Protein Expression

I want to start by saying I wasn’t sure why everyone hated DAVID, but I understand now guys! I used DAVID to make GO terms to enter into REVIGO to visualize changes in protein expression based on gene enrichment from days 11 and 13 in silo 2 based on Rhonda’s NMDS Plot:

I produced this plot with REVIGO based on proteins changed by more than 10, which is arbitrary but it seemed like a decent visual cutoff based on values in my table, plus this is preliminary analysis. I left the side bar on the plot since all points weren’t labelled and I figured it’s always easier to crop anyway!

I’m still trying to understand this plot, but it looks like there was over representation for proteins that had to do with reproduction and muscle development. I made separate plots for proteins that increased in expression and decreased in expression which can be found at the end of my jupyter notebook here.

I’m going to continue playing with this data and try to identify changes in protein expression on day 9 since it looks like differentiation between silos began to occur here.