RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Large-scale RNA interference (RNAi) experiments utilizing short-interfering RNA (siRNA) technology are increasingly prevalent for gene knock-down and screening.
• The efficacy of siRNA reagents relies heavily on oligo sequence and structure, which are determined by proprietary algorithms.
• Evolving genome annotations can render existing siRNA oligos obsolete, impacting experimental reliability and data interpretation.

Purpose of the Study:

• To introduce RNAiAtlas, a novel software and database tool for exploring, analyzing, and distributing large-scale RNAi libraries.
• To provide the latest genome annotations and historical data for RNAi reagents.
• To offer specific on-target analysis, including design quality, potential side effects, and off-target predictions.

Main Methods:

• Development of a comprehensive database (RNAiAtlas) integrating RNAi library data with up-to-date genome annotations.
• Implementation of algorithms for on-target analysis, assessing siRNA design quality, side effects, and off-target binding.
• Curation of historical annotation data to track changes and their impact on oligo relevance.

Main Results:

• RNAiAtlas offers a centralized platform for accessing and analyzing large-scale RNAi libraries, currently focused on the human genome.
• The tool provides current and historical annotation data, crucial for re-annotating and validating siRNA reagents.
• Detailed on-target analysis results, including design metrics and off-target predictions, are available for each oligo.

Conclusions:

• RNAiAtlas addresses the critical need for up-to-date annotation and analysis of RNAi reagents in large-scale studies.
• The tool enhances the reliability and interpretability of RNAi screening results by accounting for genome annotation changes.
• RNAiAtlas serves as a valuable resource for researchers utilizing RNAi technology, facilitating more accurate and robust experimental design and analysis.