The Functional Genomics Lab 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
- Software and Analysis Tools
- Assays
- Robotic Platform
- High-Content Imaging and Analysis Platforms (in progress)
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
- Ambion Silencer Select Human Druggable Genome siRNA Library V4
- Dharmacon Human ON-TARGETplus siRNA Transcription Factors Library
- Dharmacon Human ON-TARGETplus Epigenetics siRNA Library
- Ambion Silencer Select Human Ubiquitin 96 siRNA Library
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
Assays that explore one aspect of morphology or function/loss of function.
Pathway reporter assays
Examples: luciferase, beta-lactamase
Assays using a specific read-out mechanism to “report” data, or “reporter assays.”
Complex phenotypes
Examples: high-content imaging, cell cycle, translocation
Assays that explore more than one aspect of morphology or function/loss of function, usually a process with two or more steps.
3-D physiologically relevant models
Representation of 2-D and 3-D RNAi invasion screening data. The two panels are shown 24 hours after Matrigel addition. The left panel shows a well with a breast cancer organoid with an siRNA targeting MMP9 (siMMP9). The right panel shows a 3-D organoid targeted with a non-targeting siRNA AN2. These two siRNAs will be used as negative and positive controls for data analysis.
Robotic Platform
- Liquid handlers, washers and dispensers
- EnVision and Pharastar Multilabel Reader (PerkinElmer)
- Measures luminescence, fluorescence, fluorescence polarization, absorbance and time-resolved fluorescence
- ImageXpress Micro XL confocal high-content imager (Molecular Devices)
- Automated microscope used for the acquisition and analysis of cell-based images in relatively high throughput
Schematic illustration of the RNAi robotic platform.
Photograph of the RNAi robotic platform.