Genomics

UofL Genomics Facility Objectives and Resources:

The UofL Genomics Facility is located in the Clinical Translational Research Building Labs 227 F-H on the UofL Health Science Center Campus. It has been operational since Spring 2001 under the direction of Dr. Wolfgang Zacharias. The facility houses Affymetrix and Agilent microarray platforms and Ion Torrent NextGenSeq instrument system. It is staffed with a full-time Facility Manager (Sabine Waigel), two Research Technologists (Vennila Arumugam; Sreelatha Reddy), and a Data Analysis Specialist (Xiaohong Li). The team provides provide administrative support, project logistics and management, technical assistance in platform-specific sample processing and hybridization, as well as data collection, analysis and storage. Services offered include microarray-based global RNA or microRNA expression analyses, SNP profiling, whole-genome NextGen sequencing methods, quantitative real-time PCR ssays, and assistance in data analysis and mining.

The Objectives of the Facility are:

1. To provide high-quality services for microarray-based gene expression, genotyping, and NextGenSeq analysis for UofL users;

2. To continuously incorporate the newest genomics products and analysis tools into the menu of services provided;

3. To educate and train users in applications, strengths, and limitations of microarray and genomics technologies;

4. To assist users in experimental design, sample processing, and data analysis;

5. To maintain close intellectual and logistic interactions with the KBRIN Bioinformatics Core to support customer needs in experimental design, data analysis and interpretation;

6. To provide logistic support for grant applications and manuscript preparations applying microarray and genomics technologies.

Instrumentation in the Facility include an Affymetrix Microarray System with Affymetrix GCS 3000 Scanner 7G plus Autoloader, two Fluidics Stations 450 and Hybridization Oven 640; an upgraded Agilent Microarray Scanner G2505C with 2 µm resolution capability plus Workstation and Hybridization Oven G2545A; an Ion Torrent PGM (Personal Genome Machine). Access to the Illumna NextSeq whole genome sequencing platform is provided through collaboration with the UofL Center for Genetics and Molecular Medicine NextGenSeq lab. In addition, a Covaris S220 Ultrasonicator, a Sage Science Pippin Prep, an Agilent Bioanalyzer 2100, a Nanodrop ND-8000, three Applied Biosystems PCR Thermocyclers 9700, and an Applied Biosystems ViiA™ 7 real-time PCR System are available. The Facility has licenses for the latest versions of the following data analysis software packages; all of them can be accessed by the user community: GeneSpring GX v12.5 (Agilent Technologies); Partek Genomics Suite v6.6 (Partek, Inc.); MetaCore & MetaDrug (Thomson Reuters, Inc.).

The UofL Genomics Facility has regular interactions with other Core Facilities and Research Centers on Campus. Also, the close relationship with the Tissue Biorepository in the J.G. Brown Cancer Center enables access to human tissue samples with known pathologic characteristics and appropriate control specimens. The Facility continues to regularly organize and hold workshops on campus to train and update researchers in various genomic techniques and different data analysis applications.

The Facility also continues to manage the Campus-wide Life Technologies Supply Center. Reagent and supply items from Life Technologies, Invitrogen, ABI, Ambion, Gibco and Molecular Probes are ordered for a $6 flat rate shipping charge to be delivered to our Supply Center for individual investigators; popular items are stocked. The Facility Director Dr. Zacharias is a member of the UofL Institutional Service Center Task Force, with the mission to re-organize, define, and provide guidelines for classification and management of UofL Service Centers.