Supporting Information S1 - RNAi Experiments in <em>D. melanogaster</em>: Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs

Statistical analysis on a randomized genome shows that it is likely that distinct sequences from the same gene map closely elswhere on the genome, demonstrating that non-overlapping dsRNA constructs derived from the same gene can share a common off-target. 99 randomly-chosen genes were analysed for these -based on sequence similarity- off-target effects using defined scoring rules. Our results show that non-overlapping cDNA sequences of randomly chosen genes have a high prevalance of sharing off-targets in pre-mature and in exon sequences of other genes. A freely available website is provided to avoid these off-target effects and to identify “clean” combinations of dsRNA constructs derived from the same gene to down regulate any gene of interest. (6.68 MB DOC)