E-RNAi

E-RNAi designs and evaluates double-stranded RNA (dsRNA) constructs for RNA interference (RNAi) experiments to optimize specificity and efficacy and minimize off-target effects across 12 diverse organisms, including Drosophila melanogaster, Caenorhabditis elegans, Schmidtea mediterranea, Acyrthosiphon pisum, human studies, and medically relevant vectors such as Anopheles gambiae and Aedes aegypti.

Key Features:

• Organism coverage: Supports dsRNA design and evaluation for 12 diverse organisms including Drosophila melanogaster, Caenorhabditis elegans, Schmidtea mediterranea, Acyrthosiphon pisum, human studies, Anopheles gambiae, and Aedes aegypti.
• dsRNA design: Designs dsRNA reagents aimed at high specificity and efficiency with minimal predicted off-target effects.
• Target sequence evaluation: Performs computational evaluation of target sequences based on predicted performance characteristics.
• Secondary reagent design: Supports development of secondary RNAi reagents for experimental validation.
• Pooled siRNA evaluation: Evaluates pooled siRNA reagents for collective performance and potential off-target interactions.
• Batch design: Enables batch design processes for generating multiple RNAi reagents.
• Quality control: Implements stringent quality control of dsRNA constructs with assessment of potential off-target effects.
• Pre-designed reagents: Provides access to pre-designed dsRNAs for use in experiments.
• Output formats: Generates results as downloadable HTML reports and tab-delimited files.

Scientific Applications:

• Functional genomics: Enables RNAi-based interrogation of gene function across model and non-model organisms.
• High-throughput RNAi screens: Supports genome-scale RNAi screening efforts to identify gene functions and phenotypes.
• Genome-wide characterization in Drosophila: Facilitates characterization of predicted genes to identify essential genes and novel pathways related to cell growth and viability.
• Validation experiments: Supports experimental validation using secondary RNAi reagents to confirm phenotypic findings.
• Pooled library assessment: Assists evaluation of pooled siRNA libraries for collective efficacy and specificity.

Methodology:

Computational evaluation of target sequences for predicted performance characteristics and off-target effects; design of primary and secondary dsRNA reagents; batch design and pooled siRNA evaluation; generation of downloadable HTML reports and tab-delimited files.