In this week’s episode, we give an update on our libraries being prepped and sequenced by NWGC: libraries accounting for sampling day and infection statuses. Additionally, we talk about the plan for when sequence data arrives in August/September.
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
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.
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.
This week we discuss our plan of having three pools sequenced and next steps going forward. Three pools for the current three libraries are as follows:
- uninfected from Day 9 (before temperature treatment began)
- infected from Day 9 (before temperature treatment began)
- “MasterPool” : 10 samples. One sample per each of the following treatments:
- uninfected, day 12, cold
- infected, day 12, cold
- uninfected, day 12, ambient
- infected, day 12, ambient
- uninfected, day 12, warm
- infected, day 12, warm
- uninfected, day 26, cold
- infected, day 26, cold
- uninfected, day 26, ambient
- infected, day 26, ambient
This week I speak with Genevieve Johnson, a MS student at University of Alaska, Fairbanks. We talk about her thesis work on population genetics of Alaskan Tanner Crabs, her experience taking crab samples on a vessel, and her thoughts on her future.