The cycle threshold (Ct) values for each replicate were transformed to relative concentration using the estimated standard curve function (SDS 2.1, Applied Biosystems) and normalized based on GAPDH real-time data from the same samples to account for well-to-well variability.
Replicates were transformed to log2 normalised mean expression (NME), and gene symbols were assigned using the mouse4302.db library in R. Using the background gene assignments from section 'GO Analysis', 1000 genes were drawn at random, and the median of each tissue/cell expression profile for these genes was calculated from the NME of all samples.
Specifically, all raw signal intensities were first transformed to log values, then log intensities for replicate hybridizations were normalized using quantile normalization [ 81].
ΔCq replicates were then exponentially transformed to the ΔCq expression after which they were averaged ± standard deviation.
For fold comparisons, the measurement values were normalized to the respective individual replicate samples of the control group and transformed to a log2 scale.
Obtained Cq values per replicate within line (or pool) and treatment were transformed to calibrated normalized relative quantities (CNRQ) following Hellemans et al. (2007).
Variables were transformed to attain normal distributions.
For the superinfection control, pSV110 was transfected into Vero cells, superinfected with HP66 Pol-mutant virus (which is unable to replicate) and transformed into bacteria for blue/white colony screening.
The set splits between these original compositions and feats of musical mimickry, whereby Benn transforms his voice and sound to replicate Coldplay and Duran Duran, the Rolling Stones and James Blunt ("the only man alive who is his own rhyming slang").
HSV-1 viruses carrying mutations in the gene encoding the vhs protein, UL41, display a relatively minor reduction in the ability to replicate in most transformed cell lines [26], [27], [39].
