Crab Analyses Progress

I made some progress in getting new results for the crab part of my thesis. I ran DESeq2 on libraries 8-11 based on infection, but taking temperature into account. I then took those results and contrasted the two temperature treatments to get an effect of temperature on infection gene expression. I also am trying to do time-series with the individual crab RNAseq… and that’s been a bit tricky because in some cases we don’t have any replicates, and in ones where we do, there are three time points and I’m struggling to figure out how to analyze them… links to Rmd and results files in post:

DESeq2 on libraries 8-11 based on infection taking temperature into account:

Rmd: scripts/DESeq-libraries8-11.Rmd
.HTML preview: /scripts/DESeq-libraries8-11.htm

Heatmaps are viewable in the .html linked above^

Infection comparison taking temperature into account
DEGlist (.tab)
analyses/DEGlist-infection_temp-libs8-11.tab

DEGlist (.txt with Trinity_ID column):
analyses/DEGlist-infection_temp-libs8-11.txt

With count data:
/analyses/DEGlist-inf-temp-libs8-11_counts.tab

Annotated with transcriptome v. 1.5 blast output and uniprot-GO:
analyses/DEGlist-infection_temp-annot.tab

Contrast temperature treatments from the above results:

DEGlist (.tab)
analyses/DEGlist-contrast_temp-libs8-11.tab

DEGlist (.txt)
[analyses/DEGlist-contrast_temp-libs8-11.txt(https://github.com/RobertsLab/paper-crab/blob/master/analyses/DEGlist-contrast_temp-libs8-11.txt)

With count data:
analyses/DEGlist-contrast-temp-libs8-11_counts.tab

Annotated with transcriptome v. 1.5 blast output and uniprot-GO:
analyses/DEGlist-contrasttemp-annot.tab

Some processes present in the list of DEGs that were able to be annotated (43 genes) with uniprot-GO:

  • apoptosis
  • cellular response to decreased oxygen
  • transcription activity
  • defense response to gram-negative bacterium
  • cell proliferation involved in immune response
  • response to glucose starvation

Time series with individual crab RNAseq data attempts:

Rmd: scripts/DESeq-time-series.Rmd

.HTML: scripts/DESeq-time-series.html

To Do for time series:

  • try to figure out how to plot gene counts of crab ABC over time
  • Gene list for ABC vs GHI (I think I have this… but I think because it’s two temperatures at two time points, I have to do what I did above for libraries 8 -11 where I do the initital deseq, and then do a contrast to get the final gene list)
Written on June 17, 2020