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Functional Genomics Shared Resource
516.367.5417 or 5418
The primary goal is to offer cutting-edge RNAi technologies/resources and CRISPR reagents. The Core provides guidance, reagents, techinical support, and data analysis to enable researchers to perform shRNA screens. The screening process is designed to be a collaborative endeavor between the Core and Investigators. Screening is carried out at the Core. Core personnel will be available throughout the screening process to discuss design, implementation, progress, post-screening analysis, and most importantly, troubleshooting problems as they arise. Careful planning to derive a rational RNAi screen design increases the likelihood of the screen to reflect study objectives. Full service pooled shRNA screening is available (please inquire).
There is a range of RNAi tools and reagents that are available to investigators in this core, including shRNA-based reagents, as well as siRNA and dsRNA libraries.
- For whole genome screening, the facility has the 4th-generation shRNA libraries constructed by Dr. Gregory Hannon’s laboratory for targeting the human and mouse genomes. The 4th-generation designs are derived using the shERWOOD shRNA prediction algorithm, which was derived using >250,000 measurements of shRNA efficacy, the largest collection of shRNA functional data available to date. These collections will be available in both pooled and individually arrayed formats.
- The construction of a 5th-generation shRNA library is in progress and should be completed by June 2015. These reagents contain small RNAs based on Sherwood predictions incorporated into a shRNA backbone that has been optimized with modifications that strongly increase mature shRNA levels and knockdown efficacy. 5th-generation libraries targeting both the human and mouse genomes will be available.
- A set of lentiviral shRNA vectors with an array of promoters is available.
- The Shared Resource will furnish high-titer viruses for screening.
The Shared Resource provides access to high-throughput instruments for RNAi screening and post-screening validation studies:
- Agilent BioAnalyzer
- Biomek NX Liquid Handler
- MACSQuant FACS analyzer
- Perkin Elmer Enspire Plate Reader
- Miseq Illumina Sequencer