Initial PDD trials and probe set analysis. A: Top: Two qPCR primer pairs (red arrows), rRNA-A and rRNA-B, flanked the target sites for depletion probes (blue bars), while the rRNA-C primer pair was located about 100 nt away from the nearest target sites. Bottom: qPCR ΔCt values (untreated relative to PDD-treated libraries) from the three rRNA sequences and two mRNA controls. Error bars are the standard error of the mean. B: Fifty depletion probes were analysed for Tm of hybridization with intended rRNA targets (black) and likely off-target sites (red) in the transcriptome using OffTarget_Tm. The probe that later failed to deplete its target is indicated (red cross).