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Genomics High-Throughput Facility

Director: Suzanne Sandmeyer, Ph.D.
Telephone: 949-824-7571
Email: sbsandme@uci.edu

Facility Manager: Melanie Oakes, Ph.D.
Telephone: 949-824-6023
Email: mloakes@uci.edu

Bioinformatics Core Director: Jenny Wu, Ph.D.
Telephone: 949-824-6023
Email: jiew5@uci.edu

Mailing Address
340 Sprague Hall
University of California, Irvine
Irvine, CA 92697

Website: http://dmaf.biochem.uci.edu/

Overview

The UCI Genomics High-Throughput Facility (GHTF) has been in operation since 1999 and currently offers microarray and next generation DNA sequencing support for clients within and outside the University of California system. Depending on client needs, the facility can prepare mRNA, small RNA, genomic, ChIP, methyl and exome sequencing libraries. GHTF staff have experience with multiple strategy options for exome enrichment, ribosomal RNA depletion and generation of multiplex libraries in order to insure maximal return of data from experiments.

Instrumentation

The GHTF is equipped with a Covaris S2 focused sonicating shearer; Sage Sciences Blue Pippin electrophoresis system for DNA sizing and protein fractionation, NanoDrop 1000 Spectrophotometer, Qubit fluorometer, MJ Research Tetrad thermalcycler, Agilent 2100 Bioanalyzer, and Agilent MX PRO RTPCR to facilitate the preparation of libraries and quality testing and final titration of samples. The Fluidigm C1 single cell autoprep system for capturing single cells and preparing templates is available for single cell genomic applications. The Affymetrix microarray platform is utilized for gene expression studies, and analyzing known DNA SNPs and CNVs. Sequencing is currently performed using the Illumina HiSeq 2500 with a dual mode system for either high output or rapid mode sequencing. For long reads, the GHTF offers Pac Bio RS II sequencing, a capability that is useful for whole genome assembly, targeted sequencing and for studying base modifications. Digital gene expression and miRNA analysis is performed on the NanoString through campus shared access.

Software and Bioinformatic Analysis

All sequence data from the GHTF are piped to the Institute for Genomics and Bioinformatics (IGB) where they are analyzed using an Illumina pipeline or PacBio RS software. The IGB is under the supervision of Professor Pierre Baldi (UC Irvine, Information and Computer Sciences; Director, IGB). Data are reported to users as aligned or not aligned fastq files depending on user specification. Several software programs including Genomics Workbench (CLC Bio) and JMP Genomics (SAS) are installed in the GHTF for client data analysis. Clients of the GHTF have access to the campus high performance computing (HPC) cluster for analysis of sequences involving large amounts of data processing. The computer cluster is a shared computing cluster supervised by a GridEngine scheduler and has ~2000 64 bit cores including 25 nodes of 64 cores with an aggregate 8.8TB RAM and 500 TB storage in a Gluster distributed filesystem. Clients have priority on four 512 GB computing nodes with shared access to the rest of the cluster via a “Free Queue” system that gives users access to maximum computational power as it harnesses unused cycles throughout the cluster regardless of ownership/assignment.

Staff

Dr. Suzanne Sandmeyer (Professor, Dept. of Biological Chemistry) is faculty director of the GHTF, and Dr. Melanie Oakes (PhD, Dept. of Biological Chemistry) is the facility manager and provides pre- and post-consult for GHTF users. In addition, GHTF bioinformaticist, Jenny Wu, Ph.D., supports clients in post-pipeline analysis on a recharge basis. Consultation for planning experiments and for grant writing in the areas of microarrays, next generation sequencing and bioinformatics and statistics is available and encouraged.

Classes

The GHTF offers monthly/quarterly training classes and tutorials in using Linux and Open Source software on the HPC cluster as well as Bioinformatics (in conjunction with HPC staff) and also offers classes in BigData processing (with faculty in Information & Computer Sciences). The GHTF is committed to bringing new technology platforms to the campus and regularly sponsors technology seminars.

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