This post contains a slightly modified RNeasy Kit protocol. I want to use the Qiagen RNeasy Micro Plus Kit on 4 crab hemolymph pellet samples and the four corresponding supernatant samples (GitHub Issue 577). The goal is to see if there is any RNA in the supernatant samples and if that can help increase the RNA yields for each crab sample. The supernatant samples (~1ml each) will be transfered to 15ml falcon tubes and the volumes of reagents likely need to be changed (GitHub Issue ). I will be using RNA carrier for both supernatant and pellet samples. (Sidenote: just realized I didn’t use QIAshredder columns when I did the RNeasy protocol previously. I have added that to my figure.)
I’ve been working on extracting the clusters out from my heatmap and finally succeeded with this R script!
|Mean Protein Abundance||181.025||168.728||284.94||301.742|
distfun = function(x) as.dist(1 - cor(t(x), use = "pa"))
Question: Should I get error rates for the mean protein abundance of each cluster and silo?
I’m currently working on doing the same thing with the ASCA temperature influenced proteins (the ASCA table requires some different reformatting).
I had a lot of trouble trying to make a venn diagram in R (here is my attempt…). I did use the previous script to sort out a list of the proteins in each temperature, but ultimately I decided to refer back to Emma’s paper (2) and use Venny (2) the same way she did.
(1) Oliveros, J. C. Venny. An interactive tool for comparing lists with Venn’s diagrams.
https://bioinfogp.cnb.csic.es/tools/venny/index.html (accessed February 13, 2019).
(2) Timmins-Schiffman, E. B., Crandall, G. A., Vadopalas, B., Riffle, M. E., Nunn, B. L., Roberts, S. B. (2017). Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. Journal of Proteome Research, 16(9), 3298–3309.doi:10.1021/acs.jproteome.7b00288.