Research & Training

Microarray

Leader

William Wachsman, MD, PhD
Associate Professor of Medicine
Phone: (858) 552-8585, x2628, e-mail: wwachsman@ucsd.edu

Co-Leaders

Nick Webster, PhD
Professor of Medicine
Director, VA Genechip Core Facility
E-mail: nwebster@ucsd.edu

Core Contact: Jorge Valencia
Lab Manager
Phone: (858) 552-8585, x7202 or x7100, e-mail: genechip@vapop.ucsd.edu
Core Location: Stein Clinical Research Building, Room B066
Website: http://www.vmrf.org/researchcenters/microarray-ngs/microarray-ngs.html

Gary Hardiman, PhD
Assistant Professor of Medicine, Director, BIOGEM Laboratory
Phone: (858) 822-3792, e-mail: ghardiman@ucsd.edu
Core Location: Leichtag Family Foundation Research Building, Room 172

Y-T Liu, PhD
Assistant Adjunct Professor of Medicine
Director, Biomarker Core Laboratory
Phone: (858) 534-9972, e-mail: ytliu@ucsd.edu
Core Location: Moores UCSD Cancer Center, Room 5314

Service profile

  • Gene expression profiling
    • VA GeneChip Core: Affymetrix GeneChips, NobleGen arrays, Invitrogen microRNA arrays
    • BIOGEM: Illumina BeadChips, GE Codelink arrays, Agilent arrays, ABI arrays, and custom spotted arrays
  • DNA assays: SNP mapping arrays, GenFlex Tag arrays, resequencing arrays, and genome tiling arrays
  • Promoter arrays
    • VA GenomeChip Core: NimbleGen-based ChIP-on-Chip assays
    • BIOGEM: Spotted array ChIP-on-Chip assays
  • Slide array scanning services through Biomarker, BIOGEM, and VA GeneChip Cores
  • Ancillary services: BIOGEM and VA GeneChip Cores offer Agilent Bioanalyzer and Nanodrop analyses; BIOGEM has a repository of cDNA and genomic libraries
  • Consultation for experimental design and assistance with project preparation
  • Training and education (contact any of the resource leaders to be placed on mailing list for announcements)

Equipment profile

  • BIOGEM - Illumina Sentrix array system; Agilent microarray system; GE Codelink system; ABI 1700 microarray analyzer, and Affymetrix GMS417 spotted arrayer; Agilent 2100 Bioanalyzer; NanoDrop spectrophotometer; Qiagen BioRobot 3000 workstation; Molecular Dynamics/Axon GenePix 400 scanner
  • VA GeneChip Core - Affymetric GenChip ® System; Biomicro Maui hybridization station; Molecular Dynamics/Axon GenePix 4000B scanner; Agilent 2100 Bioanalyzer; NanoDrop spectrophotometer
  • Biomarker Core - Molecular Dynamics/Axon 4000B GenePix scanner

Overview

High-density microarrays permit analysis of thousands of elements simultaneously. This shared resource provides access to a panoply of microarray services to enable investigators' research. These include expression profiling of specimens for mRNA or microRNA; ChIP-on-chip assays of promotor function; directed or global SNP determination; DNA resequencing assays; and microarray-based proteomic assays. The facility has multiple platforms for microarray analyses and implements the latest array-based methods, so that investigators can perform their research at the cutting edge of the technolgoy in a cost-effective manner. The facility leadership also provides consultation to Cancer Center members on the design of microarray experiments and assistance with project preparation requiring input on specific microarray tools and methods. The resource provides training to investigators on microarray methods, tools, and analyses through courses, workshops, and seminars.

We gratefully acknowledge the support of the Department of Veterans Affairs and the San Diego Venterans Medical Research Foundation, without which this endeavor would not be possible. Links: San Diego VA Research and San Diego VMRF.