Crab Project - What I did for PCSGA 2019

In this post I will detail what I did for PCSGA 2019. I did some new analyses and found some new results from our first assembled transcriptome.

New BLAST

Steven made a BLAST database from the Dinophyceae proteins (Dinophyceae is class under which dinoflagellates are), and did a BLASTx against the first assembled transcriptome (Day 26, infected and uninfected, cold and ambient).

I used this script to separate the transcriptome into putative crab and putative Hematodiniium genes: sep_crab-hemat-genes.Rmd

That script resulted in the following files:

• crab-blastx-sp.tab
• hemat-blastx-sp.tab

Annotating BLAST outputs

In jupyter notebooks, I annotated the two blastx outputs (crab and Hematodinium) with GOslim terms.

• 091419-crab-BLAST-to-slim.ipynb
• 091419-hemat-BLAST-to-slim.ipynb

I then used the following R script to create files for creating pie charts for biological process GO slim terms:
091519-crab-hemat-GOslim.Rmd

The script resulted in the following files:

• crab-GOslim-count.csv
• hemat-GOslim-count.csv

Creating pie charts

I used the count.csv files to create pie charts in google sheets:

• crab-GOslim-pie
• hemat-GOslim-pie

For the talk, I went more in-depth into the “stress response” slice in the crab GOslim pie. I made a table of some crab genes with notes on their names and functions, and links to the uniprot database on those genes:

• crab-genes

The ones highlighted are the ones I chose to talk about in the talk.

The talk and slides

Link to final google slides: Crandall_Wed_1645

Link to slidedeck on figshare: Effects_of_Bitter_Crab_Disease_on_the_gene_expression_of_Alaskan_Tanner_Crabs

Thoughts on talk

It was supposed to be 12 minutes, with 3 minutes for questions. I have no idea how much time I took, but I did get 2 clarifying questions at the end of the talk.

It was my first time presenting at a conference, and my slot was on day 2 (Wednesday) at 4:45pm. It was a struggle to stay energized and it was also a struggle to stay calm - I was really nervous!

I think I had good background information and that I explained things fairly well, but I wish I had gone a little more in depth into the genes that we found. I also think that for next time, I need to find ways to combat the nerves because they got a bit in the way of my ability to speak at the beginning - I collected myself well-enough after the third slide or so… but I want to improve!