Evidence for a likely sample switch in the RNA-seq dataset (or not)

I've been working on the toxin/antitoxin manuscript, trying to extract all the conclusions from the RNA-seq data trove. We have two odd results, and I now think they are both best explained by a sample switch in the first set of samples.One odd result that the former post-doc drew my attention to is that, when the antitoxin is deleted, expression of the competence genes appears to be down at the last time point ('M3', 100 minutes incubation in MIV competence-induction medium).The other odd result, which I just discovered a couple of days ago, is that, when the toxin gene is deleted, expression of the competence genes appears to be up at the second time point ('M1'; 10 minutes in MIV).Each of these results is based on the mean of three biological replicates (samples pf the same strains cultured on different days). I now think that they're reciprocal consequences of the same problem - switched identities of one pair of samples prepared on the same day.History:I was originally focusing on the apparent up-regulation in the toxin deletion, which I discovered in comparisons of the toxin ('toxx') and toxin+antitoxin ('taxx') knockouts. I was looking at this comparison because it's the only one where we would expect to see any expression differences that might be caused by action of the antitoxin on genes other than the toxin, and I wanted to know if we could rule these out.The former summer undergrad had done pairwise comparisons of all the different mutants we'd test...
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs