What we learned from the RNAseq data: Part 1

So, we did a massive RNAseq study, with 124 samples ofH. influenzae cultures at different growth stages, in the rich medium sBHI and the competence-inducing medium MIV, and with wildtype or mutant genes affecting competence. (You can use the Search box to find all the previous posts about this work...) Here I specifically want to think about what we learned about competence from the competence-induced cultures (cells transferred from sBHI to MIV). We sampled cultures at the T=0 point indicated by the star in the above diagram, and the 10, 30 and 10 minute times in MIV. I'll consider the results for strains with knockout mutations in the competence-regulating genessxy andcrp, but not for the toxin-and antitoxin mutants. I'm working on this because it will be a section in our manuscript about the competence-induced toxin-antitoxin system we've discovered. After describing what the RNAseq results tell us about the general features of competence regulation, the manuscript will go on to describe what they tell us about expression of the toxA and toxT genes.About 15 years ago we used microarray analysis in a very similar study (Redfield et al 2005); the diagram above shows the sampling strategy from that work. Here I want to focus on how the new RNAseq results affect these conclusions - what's strengthened, what's changed. This will be the first time we've described the RNAseq work in a publication, so it's important to present...
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs