Functional Genomics Shared Resource

University Of Colorado Denver, Aurora CO

Investigators

Linked publications, trials & patents

Abstract

ABSTRACT Overview: Functional genomics approaches are a central pillar of modern cancer research. By enabling the manipulation of gene function and quantitative analysis of such perturbations, functional genomic tools contribute to the elucidation of genotype-to-phenotype relationships controlling cancer development and response to therapies. The field of functional genomics, a direct product of the Human Genome Project, has rapidly evolved with the advent of technologies such as RNA interference (RNAi) and rapid genome editing (e.g. CRISPR), which in turn facilitated the investigation of large numbers of genes in vertebrate cells in a single experiment. The Functional Genomics Shared Resource (FGSR) provides UCCC members access to tools that investigate gene function on a genome-wide scale; develops novel protocols and offers expertise for the use of functional genomics tools; and provides a forum for scientific exchange. By promoting collaboration in functional genomics, the FGSR serves to catalyze discoveries by UCCC members. Services: The FGSR provides reagents to members in ready-to-use and cost-effective formats. Additionally, a variety of personalized services like custom design and creation of shRNA and CRISPR panels targeting gene collections of interest, and cell engineering are also offered. Reagents/Tools: Through continuous assessment of novel technologies and UCCC members' needs, the FGSR has acquired genome-wide short hairpin RNA (shRNA), Open Reading Frame (ORF) and CRISPR libraries. The FGSR's human and mouse shRNA collections contain 176,283 clones and 138,538 clones, respectively. The ORF library contains 15,744 plasmids for overexpression of 13,082 unique human genes. The arrayed CRISPR library has 2 gRNAs per gene for 16,190 human genes. The FGSR also houses genome-wide shRNA libraries, myriad of pathway-focused shRNA panels, gene knockout CRISPR libraries like the GeCKO and Brunello and transactivating SAM libraries in ready-to-use format. Management: The FGSR is managed by the UCCC, and is overseen by the Associate Director for Basic Research. Use: Since July 2016, 318 individuals from 146 investigator laboratories have used services. Fifty-nine percent of these teams (86) were UCCC members, representing all four Programs and resulting in 80 peer-reviewed publications. Operating Budget: CCSG funding represents 43% of the annual operating budget and the remaining support is from user fees (30%) and institutional funds (27%). Consultation/Education: FGSR personnel assist members on a daily basis with experimental design and troubleshooting. The FGSR collaborates with other SRs to create robust protocols for seamless use of reagents across SRs. The website hosts a large number of very detailed protocols and bibliographic sources that are updated constantly. The FGSR also hosts `technology forums' where UCCC members are updated on the latest developments and applications in the field. Future Directions: The FGSR will continue to acquire the latest tools in the functional genomics field, such as novel CRISPR-based technologies. The service and education portfolio will be expanded via technology forums and webinars.