FA 5 Progress Report WV-INBRE - Joan C. Edwards School of ...

Program Director/Principal Investigator (Last, First, Middle): Rankin, Gary O 82Core Staff: The Genomics Core provides centralized services that would not be available to smaller labs andtraining in genomic methods of analysis. These services position research project investigators to efficientlygather critical data and analyze it with the most up to date statistical tools. Dr. Donald Primerano oversees allservices of the Genomics Core Facility, guides new protocol development and discuss proposed projectswith individual investigators. Dr. Goran Boskovic performs all microarray analyses and next generationsequencing (NGS) and library construction; he also provides training in the use of Ingenuity PathwayAnalysis software. Dr. James Denvir advises on experimental design and performs microarray and NGS dataanalyses. Conventional DNA sequencing, genotyping and genomic DNA banking are carried out by Dr. JunFan. Dr. Ivana Yang at the University of Colorado serves as an external advisor to the Genomics Core.Equipment and Lab Space: The Genomics Core is equipped with (1) an Illumina HiSeq1000 next generationsequencer with 300 Gigabase/run throughput (acquired in March 2011), (2) an Agilent Microarray Scannerwith 2 micron resolution, (3) an Agilent Hybridization Station, (4) 2 Model 7000 Sequence Detection Systems(real-time PCR), (5) a Step One Plus Sequence Detection System, (6) two Agilent Model 2100BioAnalyzers, (7) two NanoDrop spectrophotometers, (8) an Applied Biosystems 3130 Genetic Analyzer,and (9) a Luminex 100 protein detection system. All services are available to all WV-INBRE, COBRE, MUand WVU investigators. Real-time thermal cyclers and spectrophotometers are available on a sign-upbasis. The HiSeq1000 will support whole genome, whole exome, whole transcriptome (RNA-Seq) andchromatin (Chip-Seq) studies.In support of the NGS service, we have also acquired a Linux Server for data analysis and storage (40TB), a3rd Agilent BioAnalyzer for DNA/RNA quality control, an Invitrogen E-gel System for DNA/RNA purification,and a Covaris DNA Shearing System for genomic library preparation. Investigators may learn about the MUGenomics services through its web site (http://musom.marshall.edu/genomics/). The Genomics Core islocated in the Robert C. Byrd Biotechnology Science Center and has sufficient space (1200 sq ft) to provideall services.Administrative Issues: (i) All investigators must meet with the Genomics Core Staff to discuss NGS ormicroarray experimental design. Issues such as expected data, methods of analysis, biological replicates,and cost will also be discussed. (ii) Prioritization of NGS and microarray requests. We will accommodatepeaks in microarray and NGS demand by handling requests from INBRE and CTSA investigators on afirst-come first-serve basis. The Genomics Core will have discretion in determining the order of completionof experiments.Users Unique # Fees Charged Fees Paid by CenterFaculty/Post Doctorate/Staff 8 Yes YesGraduate Students 12 Yes YesUndergraduate Students 1 Yes YesPHS 2590 (Rev. 06/09)Continuation Format Page