Today we had our 4th crab meeting and discussed our short-term sequencing plan for 3 libraries (1: day 9 uninfected; 2: day 9 infected; and 3:a “masterpool” from the reamining 10 treatments). We also discussed our plan going forward with qPCR and creating libraries later and we hopefully will see some cool things with the three current chosen libraries and the qPCR.
I have the meeting recorded, just have to edit and publish it as DecaPod S1E10.
We are going to go ahead with the three libraries proposed in my previous notebook post. Sam is going to check around at the UW CORE facilities available to us. We have to use a UW facility due to budget restrictions (Pam would have to re-negotiate if we wanted to use something else, like Genewiz).
I (with Sam’s assistance and insight) will create the pooled samples such that we will have a tube for each library (3). We will then use the Speed Vac to evaporate off some liquid in order to get a specific concentration (TBD- depends on what the CORE facility requires).
Sequencing takes some time, so while we are waiting for the results to come back, I will compile databases of genomic resources. Namely, find fasta files for those closest related to Chionoecetes bairdi and Hematodinium spp. and create databses. I will also practice using Trinity and BLAST with some geoduck data that we have already so that once the RNAseq data from our crabs comes back, we’ll already have a good idea on how to execute the bioinformatic pipeline.
Once we analyze the data and pick out some genes, we will make primers and use qPCR on individuals. If we see anything that we’d like to look at more closely, we can create new libraries of individuals or pools. I also may extract more RNA since I currently have only extracted RNA from <~50% of the surviving crabs (113 crabs survived the experiment and I have extracted RNA from 51 of them).
I will be learning a lot this summer and I am really excited! Reading and praciticing occasionally doesn’t stick with me as much as actually doing things, so practicing with real data will be very helpful. Pam is also interested in learning more as well, so working with her and potentially teaching her what I learn will further enrich my understanding. Looking forward to it!