I isolated RNA from the warm crab sample tubes today!
I isolated RNA from the warm crab sample tubes today!
So last week was unfortunately not as productive as I had planned as a result of some dog-sitting shenanigans. So, to help myself get back on top of things, I’m making a list of what I want to and will accomplish this week. Firstly, tomorrow I have a presentation in my FISH 511 class, so I will be focusing on that today and tomorrow. The rest of the week will be as follows:
I did Qubit on 14 more samples today. I ran out of the RNA HS Reagent, so Pam will have to order more.
I’ll continue isolating the RNA from the subset of samples that I selected from crabs that survived the experiment.
Today I isolated RNA from the below samples:
I re-did the DIA analysis from the beginning. This time I only used settings used by Emma in her Skyline document that she sent me.
Today Steven and I recorded a little bit of us talking about the spreadsheet and how I’ll be doing the RNA isolating. What I am going to work on is an episode, or several short episodes, about the background of the project: bitter crab disease; Tanner crabs; Juneau, etc. I also am going to make a quick little intro that we can put at the beginning of all the episodes. I want to make one weekly, or at least release one weekly. And I would like to have some way to make it more easily understandable to people like my mom, or my friends. To do that I think I just have to make sure I explain what I’m talking about more. Obvoiusly I shouldn’t be putting too much time into it because the main focus is on the research itself, but I’m excited and looking forward to learning more about this outreach tool and communication strategy.
Today we had our first crab project meeting. Our plan is to meet the first Thursday of the month (subject to change if need be).
Today I began the process of isolating RNA from the “official” crab hemolymph samples, although they can change if I mess things up, because there are many extra samples.
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:
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