In this episode, we go through Grace’s GitHub repository for one of her classes in which she made some figures using BLAST results from our first assembled crab transcriptome against the swissprot/uniprot protein database, and against the nucleotide taxonomy database. Follow along as we discuss the README.md of this repository: https://github.com/fish546-2018/grace-Cbairdi-transcriptome
Check our new poster!
This poster was given at a Graduate Student Symposium at the School of Aquatic and Fishery Sciences. It encompasses the overall project outline and goals, as well as some data from our first assembled transcriptome. More information on the project and updates can be found at our website (bittercrab.science) or our podcast (DecaPod) that is now available on iTunes.
This week, I talk with Madison (Madi) Shipley.
She is a graduate student (MS) in the School of Aquatic and Fishery Sciences, at the University of Washington. We talk about her thesis work of developing a management strategy evaluation for Tanner crab in the Eastern Bering Sea, her job with the Natural Resources Consultants Incorporated, how she got into the crab world, and her plans after receiving her degree. She also shares some of her at-sea experience with surveying in the Bering Sea.
This week we talk about transcriptome assembly (with our new RNAseq data from NWGC!!) and next steps. Also, we decide that Qiagen RNeasy Kit works pretty well for extracting RNA, and will be used to create the remaining libraries for the project.
Today I ran BLAST with the bad fasta from the Trinity run from last weekend. Will look more at the notebook Steven sent me to do the BLAST stats, goslim, contigs, go slim tables, etc. I also have been getting some input from Sam as to how best to manage adding new Qubit data to a master file consisting of all the hemolymph sampling data joined with the Qubit data results. Finally, I tested out the RNeasy Plus Micro Kit on 4 samples from Day 26, and ran the Qubit.
This week Pam tells us about her recent experience on a survey on the Bering Sea, and we discuss our new plan.
The original RNA extraction method using RNAzol RT resulted in low RNA yields, as well as contaminated samples, likely due to excess salts. We have submitted a pooled sample to the NWGC for library prep and sequencing. The pooled sample consists of samples from day 26 (samples were taken in triplicate) from cold and ambient infected and uninfected treatments. This library will be used for gene discovery.
As we continue investigating better methods for RNA extraction, we will create libraries that will be used for comparison between treatment groups.
2015 Oysterseed Project:
- Figure out Skyline DIA with Emma (plan for 9/6/18)
- Analyze 2015 Oysterseed data
- Lyophilizer is fixed –> use this along with Tri-Reagent on selected pelleted and supernatant samples
- Continue to learn more background information on C. bairdi, Hematodinium, Bitter Crab disease, etc.
- Practice qPCR to test shellfish primers; learn more about qPCR