The Functional Genomics Core (FGC), a key component of the COBRE Center for Targeted Therapeutics (CTT), enables current and future COBRE faculty to conduct high-throughput target discovery and validation studies through sophisticated functional genomics technologies. These include target identification through phenotypic selection of Transdominant Genetic Regulators (TGRs), transcriptomic and epigenomic analysis through Next-Gen Sequencing (NGS) and microarray-based approaches, vector generation, lentiviral transduction, cell line modification and gene expression analysis. The FGC will support all four COBRE Projects via three Specific Aims:
Aim 1. Train COBRE investigators; assist in designing and implementing the strategies for TGR-based target identification using short hairpin RNA (shRNA), single guide RNA (sgRNA) and Genetic Suppressor Element (GSE) libraries. The FGC will provide several transcriptome- scale human sgRNAs, shRNA and GSE libraries; conduct lentiviral transduction of TGI libraries into recipient cell lines; and assist COBRE investigators with selection procedures. The FGC will also 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 in testing individual targets through shRNA transduction or siRNA transfection.
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.
Aim 3. Carry out transcriptomic and epigenomic profiling and gene expression measurement for analyzing the effects of experimental compounds and genetic inhibitors. The FGC will provide transcriptomic services through RNA-seq using Illumina NextSeq500 and microarray analysis on both the Agilent and Affymetrix platforms. The FGC will assist investigators with the bioinformatics analysis of the transcriptomic data. The FGC will also provide epigenomics analysis services, including Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-Seq) and Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq) and other NGS-based services, assist with NGS data analysis and with quantitative real-time reverse-transcription-PCR for gene expression measurements. The FGC will also support COBRE investigators in assuring scientific rigor through cell line authentication and mycoplasma testing services. 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.
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