Genomics

Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA

Investigators

Linked publications & trials

Abstract

The mission of the Genomics Shared Resource is to support Cancer Center members in their studies of DNA as well as gene expression. The Genomics Shared Resource is composed of two facilities. These are DNA Analysis, providing DNA sequencing and mouse genotyping service, and Microarray/Q-PCR, providing lllumina-based microarray analysis, as well as full-service real-time quantitative PCR. DNA Analysis: Full-service DNA sequence analvsis is provided using a 16 capillary-based instrument. PCR-based mouse genotyping is performed to characterize transgenic mice. Cancer Center investigators will soon also be provided access to next-gen sequencing, which will enable quantitative unbiased expression profiling, analysis of RNA splicing, chip-seq determining genomic targets for transcription factors, and identifying cancer-associated mutations. For mouse qenotvpinq. tail samples are delivered directly from Animal Resources to DNA Analysis. DNA is isolated and analyzed using an investigatordeveloped PCR assay followed by agarose gel analysis. Results are rapidly returned to investigators, speeding selection of desired transgenic mice, accelerating research and reducing mouse costs. Microarray/Q-PCR: Global gene expression analysis is performed using the Illumina BeadStation microarray system. Such microarray analvsis for human, mouse and rat samples is both robust and cost effective. This full-service analysis starts with investigator RNA, and returns initially analyzed data to them. Extensive additional microarray data analysis to put results in a statistical, biological, or pathway context is available from the IDM Shared Resource. Recently, global profiling of miRNAs has been introduced, and ongoing enhancements are being made in microarray analysis. Full service Q-PCR is also provided, where investigators can provide RNA and have the facility design primers and an experimental plan, ultimately retuning fold-difference data. Shared Resource staff also provide traininq on a suite of common-use instrumentation, including a multifunctional fluorescence scanner and phosphorlmager, cooled CCD blot/gel imager, near-IR (LI-COR) scanners, microplate luminometer, and Nanodrop Spectrophotometer. The Genomics Shared Resource is broadly used, having supported over 250 publications in the last funding period. In the past year, 41 Cancer Center members, representing all 4 Programs, utilized the services of the facility. Overall, $121,554 in CCSG support is requested in the first year, representing 16.4% of the total projected operating budget for the Genomics Shared Resource.