biogem

Shared Resources

UCSD High-Throughput Genomics Umbrella Core Facility (HTG-UCF)

A major paradigm shift in the research community has been the adoption of high throughput next-generation (next-gen) sequencing technologies. While it is premature to retire microarray-based technologies, the digital information generated by high-throughput sequencing is clearly leading the charge and further development of enabling technologies promises unprecedented insights into gene structure and function. The HTG-UCF currently provides access to all major microarray platforms in addition to next-generation sequencing. There are presently two separate laboratories on the UCSD campus that comprise the HTG-UCF; The Biomedical Genomics (BIOGEM) and Gene Chip Core facilities. These cores offer non-overlapping but complementary genomics technologies.

Web Sites

HTG-UCF
Biomedical Genomics laboratory (BIOGEM)
VA Genechip Facility

Personnel

Gary Hardiman, Ph.D.

Associate Professor of Medicine
Director, BIOGEM Laboratory
Email: ghardiman@ucsd.edu
Core Location: Leichtag Family Foundation Research Building, Room 172

Nick Webster, PhD

Professor of Medicine
Director, VA Genechip Core Facility
Email: nwebster@ucsd.edu
Core Location: Stein Clinical Research Building, Room B066

Core Contacts:

BIOGEM Core

Agilent and Illumina Arrays
Illumina Sequencing
James Sprague
(858) 822-4231
Email: ljsprague@ucsd.edu

Pacific Biosciences Sequencing
Colleen Ludka
(858) 822-4231
Email: cludka@ucsd.edu

Illumina Genotyping
Michael Harabaglia
(858) 822-4231
Email: mharabaglia@ucsd.edu

Autogen DNA Extraction
Mila Angert
(858) 822-4231
Email: mangert@ucsd.edu

Genechip Core

Affymetrix and Nimblegen Arrays
454 Sequencing
Jorge Valencia
(858) 552-8585 x7100
Email: genechip@vapop.ucsd.edu

Service Profile:

Gene Expression Profiling

VA GeneChip Core: Affymetrix GeneChips, NimbleGen arrays, Invitrogen microRNA arrays
BIOGEM: Illumina BeadChips, Codelink arrays, Agilent arrays (expression and microRNA)

DNA Assays: SNP mapping arrays, GenFlex Tag arrays, resequencing arrays, and genome tiling arrays

Ancillary Services: BIOGEM and VA GeneChip Cores offer Agilent Bioanalyzer and Nanodrop analyses; BIOGEM has a repository of cDNA clones.
Consultation for experimental design and assistance with project preparation

Equipment Profile:

BIOGEM Facility equipment includes:

Agilent microarray scanner.
BioRobotics MicroGrid Spotter
Agilent 2100 Bioanalyzer
NanoDrop ND-1000 UV-Vis Spectrophotometer
Illumina Bead Station 500
2 x Illumina HiSeq2000 (Next Gen Sequencer)
Roche LightCycler 480
Pacific Biosciences RS
Covaris E220
Agilent 2200 TapeStation system

For more information
http://www.microarrays.ucsd.edu/biogem/resources/

VA GeneChip Facility equipment includes:

Affymetrix 640 Hybridization Ovens (two)
Affymetrix GeneChip 450 fluidics stations (two)
Gene Chip GCS3000 high-resolution scanner with auto-loading carousel.
Agilent 2100 Bioanalyzer
NanoDrop ND-1000 UV-Vis Spectrophotometer
BioMicro Maui (MicroArray User Interface) Hybridization Station
BioMicro Maui Wash Station
Molecular Dynamics/Axon Genepix 4000B scanner
Qiagen TissueLyzer2 (two)
Genome Systems Hydroshear for paired-end library synthesis
Roche 454 Genome Sequencer FLX System
Beckman Z1 Coulter Counter for bead enrichment
Beckman Allegra X-12 centrifuge for bead deposition
BioRad thermal cyclers
PCR hoods for setting up emulsion PCR
Laminar flow hood for fragmenting samples for library prep
Turner Designs fluorimeter
PSSC 5-node server cluster

For more information
http://www.vmrf.org/researchcenters/gene-chip/core-equipment.html

Overview of the HTG-UCF:

The mission of the proposed HTG-UCF is to provide UCSD investigators with high quality standard and cutting-edge high-throughput genomic assays, as well as, consultation on experimental design. Microarray and next-gen sequencing experimentation, data acquisition and analysis require expensive instrumentation and reagents and a highly skilled team of individuals who are experts in specific components of the overall procedure. These technologies therefore lie beyond the scope of most individual laboratories and can only be made accessible to academic investigators through common core facilities. In addition to providing conventional genomic services, such cores provide essential platforms for advancing new technologies. The Biomedical Genomics Microarray (BIOGEM) Core facility and VA Gene Chip Core Facilities at UCSD have been instrumental in providing UCSD investigators access to these technologies. In particular, they have played a key role in enabling UCSD faculty to effectively compete for extramural grant support.

The UCSD-wide High-Throughput Genomics Umbrella Core Facility gratefully acknowledge the support of the School Of Medicine, the Campus Office of Research Affairs at UCSD, the Department of Veterans Affairs, the San Diego Veterans Medical Research Foundation and NIH grants DK063491, CA023100 and DK080506 without which this endeavor would not be possible.

Last Updated November 2012
By Dr. Gary Hardiman