This week I determined if I isolated RNA (detectable in one, not in the other).
This quarter I am taking FISH 521, which is the Research Proposal Writing and Professional Development course taught by Julian Olden. This class has been very helpful because it has guided me through the layout of the Crab Project and the plan of how it will all be performed. This is good becuase this is my first quarter of graduate school and I had only heard about the crab project around Thanksgiving of 2017.
I am either blind or we don’t have it, but I could not find RNAzol RT. I found all the other reagents needed, but not the RNAzol. I thought I saw it, but it was DNAzol. So the RNA isolation has to wait until either someone proves me wrong and finds it, or we order more.
Tommorrow I will be trying out RNA isolation on 2 extra Tanner crab hemolymph samples. Try protocol with 2 samples: 465 and 468 Both samples are yellow (from third sampling day) and are from crabs that are infected, immature, and held at ambient temperatures throughout the experiment.
Today I re-picked the samples that I’ll use for RNA extraction. I realized that I could easily choose samples from the same crabs across all sampling days and temperatures. I went back and amended the initial post with the new choices, so that I don’t get confused in the future.
Steven, Kaitlyn, and I met with Emma today to discuss proteomics. I’m doing DIA with 2015 oysterseed data (from the 2015 project) and Kaitlyn is doing DDA with 2016 oyster data.
I ordered two of the USB Samson Meteor Mic microphones.
I tested out the USB Microhpone Samson Meteor Mic (2016). It connects to my laptop via a USB cord. I opened up GarageBand and started a new Audio/Voice Project. There are many different vocal effects options, but I just used the basic “Narration vocal”. Press the red circle record button to begin, and press again to stop. After you are done recording, you can edit the vocal recording.
I would have made this post on the actual first day of February, but I have been sick - the neverending cold. Anyway, for this short month I have some goals I’d like to achieve:
RNA Isolation prep
Today I chose some crab samples for RNA extraction. I made a chart with the tube numbers for the samples. All crabs are immature males. Due to a massive die-off in the warm temperature treatment groups, we unfortunately only have two infected and one uninfected sample per the final two sample days. As a result, the uninfected samples will not be “pooled”.
Today the new qPCR machine arrived. Brian showed us the basics of using the machine and the software. He offered to come back anytime once we start using the machine to help answer questions specific to our project.
Today I heard back from Emma that my ~35% error rate is okay, and that there isn’t much to be done about it anyway. So now I am clear to move on to the next steps in analyzing the 2015 Oysterseed data.
Today I FINALLY finished error-checking peaks in Skyline.
I moved computers from Swan to Woodpecker. In order to be able to continue a project on a different computer, you need to File > Share > Complete. It becomes a .zip file. Upload to OWL. Open zip on new computer, and all the libraries and everything is included.
I continued with the Skyline DIA analysis of the 2015 Oyster Seed Project data.
Received Green-cap and pink-cap samples on 11/13/17