Fig. 3. qRT-PCR analysis of RNAs derived from the pilE deletion mutants. (a) Schematic showing the relative location of the primer pairs used in the qRT-PCR experiments. Tsp indicates the transcription start point; Tep indicates the transcription end point. The locations of the deletions are also indicated. (b) qRT-PCR analysis of RNA preparations extracted from deletion mutant 4 (the brick-like shading) and deletion mutant 6 (the diagonal shading). The forward primer in each case was primer 1 which assesses the relative amount of full-length (or near full-length transcript depending upon the deletion) in the sample. The data are presented as a difference in the pilE Ct scores verses the recA Ct score. The recA Ct scores were in the order of 24 cycles. A negative value indicates a lower Ct score for the pilE primer pair than that obtained for recA which equates to more RNA being present within the sample.