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Designing Controls for siRNA ,,, Experiments

anges to the gene expression profile that may result from the siRNA delivery method. Comparing cells transfected with a scrambled siRNA control to untransfected cells can reveal changes caused by siRNA delivery.

Positive siRNA Control
Ambion scientists always include a positive siRNA control in their experiments -- usually the Silencer GAPDH siRNA -- which serves to monitor siRNA transfection efficiency. When the positive control fails to elicit the expected reduction in gene expression, poor transfection is immediately suspected.

Multiple siRNAs to a Single Target
One of the best ways to increase confidence in data from siRNA experiments is to use two or more siRNAs to a single gene target. The siRNAs should first be analyzed for effectiveness at reducing target gene expression. Different siRNAs to the same gene with comparable gene silencing efficacy should induce similar changes in gene expression profile and phenotype. Any changes induced by one siRNA and not the other(s) could be attributed to off target effects. This approach is also valid for siRNA cocktails. In other words, cocktails prepared from different regions of the same gene can be used to confirm gene silencing results.

Monitor the Antiviral Response
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