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Experimental RNAi

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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MISSION esiRNA for RNAi Screening in Mammalian Cells

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

Z' factor including siRNA design quality parameter in RNAi screening experiments.

Sławomir Mazur¹, Karol Kozak

¹BIOQUANT-Zentrum, Ruprecht-Karls-Universität, Heidelberg, Germany.

|May 23, 2012

Summary

This study introduces an enhanced Z' factor for RNA interference (RNAi) high-content screening (HCS) quality assessment. The new method integrates bioinformatics and on-target analysis for more reliable RNAi screening results.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

High-content screening (HCS) with RNA interference (RNAi) is crucial for identifying gene-disease links.
Assay quality is paramount for reliable genome-scale RNAi screening.
The Z' factor is a standard metric for evaluating screening run conditions.

Purpose of the Study:

To develop an improved Z' factor calculation for RNAi HCS.
To address limitations of the current Z' factor in RNAi experiments with potential off-target effects or insufficient knockdown.
To enhance the reliability of RNAi screening for discovering gene-phenotype relationships.

Main Methods:

Extension of the existing Z' factor algorithm.
Integration of bioinformatics analysis for RNAi non-target compounds.
Inclusion of additional controls derived from on-target analysis.

Main Results:

The proposed algorithm provides a more robust assessment of RNAi HCS quality.
The enhanced Z' factor accounts for oligonucleotide (oligo) variability and lack of knockdown.
Improved screening quality assessment for genome-scale RNAi studies.

Conclusions:

The extended Z' factor offers a more comprehensive quality control for RNAi HCS.
This advancement supports more accurate identification of gene-disease associations.
The method enhances the utility of RNAi HCS in biological discovery.