The Functional Genomics Core (FGC), a key component of the COBRE, will enable current and future COBRE faculty to conduct high-throughput target discovery studies through phenotypic selection of Transdominant Genetic Inhibitors (TGIs). The FGC will also assist COBRE investigators with special molecular genetics and genomics techniques, including vector generation, lentiviral transduction, cell line modification, and gene expression analysis and profiling through QPCR, microarray analysis and RNA-Seq. The FGC will serve all four COBRE Projects via three Specific Aims:
Aim 1. Train the investigators and assist in the design and implementation of strategies for TGI-based target identification using transcriptome-scale lentiviral short hairpin RNA (shRNA) and Genetic Suppressor Elements (GSE) libraries. The FGC will provide several transcriptome-scale human shRNA and GSE libraries;conduct lentiviral transduction of TGI libraries into recipient cell lines;and assist the investigators with selection procedures. The FGC will also help produce """"""""focused"""""""" shRNA libraries of a subset of genes for preliminary high-throughput validation and prioritization of the targets identified in the initial selection, and help testing individual targets through shRNA transduction or siRNA transfection (Projects 1 and 3).
Aim 2. Assist COBRE investigators with genetic modification of cell lines for target or drug discovery or characterization through lentiviral transduction. The FGC will assist COBRE investigators in modifying cell lines for screening or analysis purposes. These modifications will include introducing fluorescent tags, promoter-reporter constructs, and the knockdown or overexpression of specific genes, in both stable and inducible formats (Projects 1, 3 and 4).
Aim 3. Carry out gene expression profiling and measurement for analyzing the effects of experimental compounds and genetic inhibitors. The FGC will provide microarray services on both Agilent and Affymetrix platforms and assist with the analysis of the microarray data. The Core will also prepare samples for RNA-Seq;interface with external Next-Gen sequencing facilities;assist with Next-Gen data analysis and with quantitative real-time reverse-transcription-PCR for validation of gene expression data (Projects 1, 2 and 3). The FGC will enable junior investigators to venture into areas of research that require sophisticated skills and years of experience, accelerating the pace of discovery and at the same time nurturing junior investigators into highly-skilled scientists.
A precise determination of the role of genes and gene products in disease processes is critical to the identification of clinically relevant therapeutic targets for a variety of diseases. Functional Genomics approaches provide an effective way to rapidly derive reliable information about the function of genes and gene products that can be controlled very specifically, and therefore with fewer side effects, by drugs.
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