Controls for RNAi Experiments

Proper RNAi controls are essential for successful RNAi experiments. We offer controls for both siRNA and miRNA experiments. Our siRNA controls, including negative and positive control siRNAs, help to determine non-specific cellular responses and optimize transfection conditions to enhance your gene silencing research. To enable clear results for miRNA experiments, positive and negative controls are available for both miRNA mimics and inhibitors.

siRNA controls  miRNA controls

For optimal results, it is advisable to use controls from the same product line as your experimental siRNA, such as Silencer Select siRNA. This helps ensure consistency and accounts for the effects of chemical modifications. If you are working with unmodified custom siRNA, Silencer siRNA controls should be used to maintain the integrity of your experiments.

Negative control siRNAs are most often a non-targeting siRNA—designed not to target any gene—for determining the non-specific effects of siRNA delivery and for offering a baseline to compare to siRNA-treated samples. Scrambled control siRNA is a sequence that has been randomly rearranged to have the same nucleotide composition as a target-specific siRNA, but also no known off-targets. Negative controls may also be a functional siRNA that is known to have no impact on your phenotype of interest, which should be determined empirically. We recommend using one or more negative controls in every RNAi experiment.

Silencer Select negative control siRNAs

• Non-targeting controls with no significant sequence similarity to human, mouse or rat gene sequences
• Chemically modified for reduced off-target effects as found in other Silencer Select siRNAs
• Tested by microarray analysis and shown to have minimal effects on gene expression
• Assessed in multiparametric cell-based assays and are proven to have no significant effect on cell proliferation, viability, or morphology in the cell lines tested

• No significant sequence similarity to human, mouse, or rat sequences
• Tested in cell-based screens and proven to have no significant effect on cell proliferation, viability, or morphology
• Recommended for use in experiments with any Silencer siRNA or unmodified siRNA 

• Negative controls that offer low, medium, and high levels of GC content to match that of the experimental Stealth RNAi siRNAs
• Medium GC is recommended for experiments using numerous unique siRNA designs

Positive controls help give you confidence in your RNAi experiments by confirming that experimental conditions were met to achieve robust silencing. Positive controls are verified siRNAs that are known to achieve high levels of knockdown (>70%), typically for a constitutively expressed or housekeeping gene. A positive control should be used to optimize siRNA delivery conditions and to reconfirm high levels of delivery in each RNAi experiment. When a positive control fails to produce the anticipated phenotype, carefully evaluate your experimental conditions and decide if some factors need to be adjusted.

Silencer Select positive control siRNAs

• Extensively tested for optimizing and monitoring transfection efficiency in human, mouse, and rat cells
• Functionally tested in several common cell lines
• Include Silencer Select siRNA modifications for enhanced specificity

Silencer positive control siRNAs

• Tested reagents targeting housekeeping genes or common reporter genes
• Recommended for use in experiments with any Silencer siRNA or unmodified siRNA
• Fluorescent options for monitoring transfection efficiency

Stealth RNAi positive controls

• Tested reagents targeting housekeeping genes or common reporter genes
• Excellent as a control for assessing knockdown and optimizing Stealth RNAi experiments

Fluorescently labeled transfection controls

To achieve the highest transfection efficiency possible, it is advised to first optimize transfection conditions for your cell lines. An siRNA or oligo with a fluorophore conjugate, such as FAM or Cy3, can be useful as a visual indicator of transfection success, especially during transfection optimization when conditions such as cell density and the amount of transfection reagent are being varied. It should be noted that intracellular fluorescence is not a substitute for quantitation of transfection efficiency as measured by knockdown from a verified positive control.

miRNA mimic and inhibitor controls are essential for verifying experimental results, helping ensure that observed effects are due to specific miRNA modulation rather than off-target or non-specific activity. To support your miRNA experiments, we offer positive and negative controls for both miRNA mimics and inhibitors.

For more optimal siRNA transfection, we have many cell type-specific transfection protocols for siRNA delivery using Lipofectamine RNAiMAX Transfection Reagent to help you get started. 

Learn more about RNAi transfection