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As with experiments using individual siRNAs, effective negative and positive control siRNAs are essential for determining transfection efficiency and to control for the general effects of siRNA delivery in these screens. Negative control siRNAs are also critical for setting the “hit” threshold that determines whether an siRNA is considered as having a positive, negative, or neutral effect in a particular assay. Because of their importance, and due in part to the fact that some negative control siRNAs may have unintended effects in a particular assay, most researchers carefully test their negative control siRNAs before choosing ones for inclusion in their screen.
Ambion now offers the Silencer® siRNA Screening Control Panel, a set of seven unique negative control siRNAs that enable RNAi researchers to identify the best negative control(s) for their cell system. These siRNAs lack similarity to nucleotide sequences in all known human, mouse, and rat genes. They have been tested in cell-based screens and proven to have no significant effect on cell proliferation, cell viability, and cell morphology, highlighting their usefulness as negative controls. An example of the effect of transfecting these controls on cell number is provided in Figure 1A.