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RNA Interference

RNAi Resources

The RNAi experts at NCATS employ scientific resources that include a variety of commercially available siRNA screening libraries; tools for data tracking, storage and analysis; and a fully automated, large-scale screening platform.

Screening Libraries

  • Ambion Silencer Select Human Genome-Wide siRNA library targeting ~22,000 genes with three individual siRNAs per gene
  • Ambion Silencer Mouse Genome-Wide siRNA library targeting ~17,000 genes with three individual siRNAs per gene
  • Dharmacon siGENOME and Dharmacon ON-TARGETplus Human Genome-Wide siRNA libraries (Thermo Scientific), with pools of four siRNAs targeted against each of ~16,000 genes in the library; “druggable genome” subsets included for focused screening of potentially druggable targets
  • microRNA mimic and inhibitor libraries

Software and Analysis Tools

  • RNAi Data Viewer
    This tool allows users to view plates, check stats, screen data and perform a variety of analyses. Access user data (restricted).

Assays

Simple phenotypes

Examples: viability, cytotoxicity

A microscope image of six live round cells is presented as an example of an assay that explores morphology or cell count.

Assays that explore one aspect of morphology or function/loss of function.

Pathway reporter assays

Examples: luciferase, beta-lactamase

A large, gene network graph is presented as an example of a signaling pathway that can be assayed using a reporter construct.

Assays using a specific read-out mechanism to “report” data, or “reporter assays.”

Complex phenotypes

Examples: high-content imaging, cell cycle, translocation

A microscope image of cells with two fluorescent markers, green and red, designed to study the interaction of two proteins within a cell.

Assays that explore more than one aspect of morphology or function/loss of function, usually a process with two or more steps.

Robotic Platform

  • Liquid handlers, washers and dispensers
  • EnVision Multilabel Reader (PerkinElmer)
    • Measures luminescence, fluorescence, fluorescence polarization, absorbance and time-resolved fluorescence
  • ImageXpress Micro XL high-content imager (Molecular Devices)
    • Automated microscope used for the acquisition and analysis of cell-based images in relatively high throughput
A schematic cartoon of a high-throughput robotic system that houses instruments required for high-content screening. These instruments include plate-based readers, plate washers and liquid dispensers.

Schematic illustration of the RNAi robotic platform.

Photograph of the RNAi robotic platform.

Photograph of the RNAi robotic platform.

Last updated: 06-25-2015
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