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UC Davis Comprehensive Cancer Center

UC Davis Comprehensive Cancer Center

Genomics

Director: Jeffrey P. Gregg, M.D. 

Video: Jeffrey Gregg, director of the Genomics Shared Resource at UC Davis Comprehensive Cancer Center,
describes the vast capabilities of the resource to assist investigators in clinical and basic cancer research.

The Genomics Shared Resource (GSR) is a core facility providing microarray, next-generation sequencing and general nucleic acid services at the UC Davis Health System and beyond.

The mission of the GSR is to serve the UC Davis Comprehensive Cancer Center by providing centralized, cost-effective and comprehensive expertise and service in the area of microarray-based and next-generation sequencing-based genomics research. This includes every level of genomics, ranging from analysis of cancer genomes with single-base resolution up through standard mRNA and miRNA expression profiling. The GSR also provides extensive data analysis and integrative bioinformatics support as well as a variety of educational opportunities. Taken together, the GSR offers a complete integrative and functional molecular profiling solution for the cancer center.

The GSR Service

Genomics Shared Resource - Jeffrey Gregg and Cliff TepperWe offer a service that provides the researcher a complete solution for gene expression analysis. The researcher only needs to provide the total RNA sample. The service includes all subsequent processing for the expression analysis. This includes the reverse transcription, amplification and biotinylation by in vitro transcription, hybridization to the array, fluorescent labeling, scanning, and preliminary analysis of the sample(s). Data will be provided in the form of the GeneChip .CEL file for each sample and an auto-filtered Microsoft Excel spreadsheet that includes the absolute expression data and the comparison data for the sample comparisons requested.

Getting started

Performing gene expression microarray experiments can be intimidating and extremely complicated, even for experienced users. Learning about the applications and pitfalls of this technology is the first step toward successful microarray experiments. For this reason, we have tried to compile as much information as possible on this website, so please read it thoroughly. In addition, we strongly recommend that researchers thinking about starting microarray experiments talk to us about experimental design, sample preparation and the nuances of gene expression microarrays before starting their experiments. We do all preliminary consultation free of charge, and we can be reached by email for scheduling consultation time (please specify that the appointment should be for a preliminary consultation). We are also always available via email to answer any questions.

The GSR provides genomics services in the following areas:

Affymetrix Microarrays

Affymetrix pioneered the microarray field by providing a turnkey solution for analysis of global gene expression, genotyping, transcriptomics and gene regulation. The GSR provides a number of services using Affymetrix GeneChips to query the genome and transcriptome.


Agilent and Other Microarrays

The Agilent microarray platform provides a reliable flexible-content system based on their SurePrint inkjet technology. Pre-printed arrays contain anywhere from 15,000 to 1,000,000 features, and custom arrays can be ordered by the researcher for the study of more focused gene-sets or non-standard organisms.


Illumina Next-generation Sequencing

Illumina’s Sequencing-by-Synthesis technology is one of the most powerful genomics technologies to emerge in recent years and has already begun to accelerate the pace of advances in basic and translational research. The GSR provides complete library preparation, sample analysis and sequencing services for the Illumina GAIIx system.


Nucleic Acid Isolations and QC

The GSR has extensive experience with the isolation of DNA and RNA from various sources (whole blood, frozen and FFPE tissue, cell lines, and others). We also routinely perform quantity and quality analysis with our NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.


Consultation and Data Analysis

Consultation is provided at an hourly rate (waived for Cancer Center members) for assistance with experimental design, troubleshooting, data analysis, results interpretation and manuscript proposal preparation. 

The data processing and analysis capabilities of the GSR are supported by an infrastructure of servers and computational workstations, as well as licenses for several commercial bioinformatic software packages. Computer time and software use can be reserved by the hour and includes free instruction and troubleshooting help.

Appointments for both consultation and use of the data analysis center can be made via  .

Genomics shared resource staff
The Genomics Shared Resource Staff (clockwise from right rear):  Dr. Jeffrey Gregg, Stephenie Liu, Dr. Clifford Tepper, Ryan Davis

We have been in operation as a core facility since 2001, and our focus is to serve the UC Davis Comprehensive Cancer Center. We also cater to the UC Davis MIND Institute and the University of California research community, as well as other academic, government and industry investigators. Each member of the GSR team contributes a complement of unique backgrounds and skills that synergize to provide comprehensive genomic analysis solutions.


Jeffrey P. Gregg, M.D. (Director)
Dr. Gregg is an associate professor in the Department of Pathology and Laboratory Medicine, director of the UC Davis Health System Molecular Diagnostics Laboratory, and acting director and vice chair of clinical pathology. He founded the GSR in 2001 and brings to the Resource a sustained record of research experience and scientific leadership, as well as the expertise and vision of a pioneer in genomics technology. In addition, his clinical experience with the application of molecular and genomics technologies for clinical diagnostics give him particular insight into the translational capabilities of these technologies. Dr. Gregg is available by appointment for consultation.
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Clifford Tepper, Ph.D. (Technical Director)  
Dr. Tepper is an associate research biochemist in the Department of Biochemistry and Molecular Medicine and has served as the technical director of the GSR since 2002. He is a molecular and cellular biologist with extensive cancer research experience in signal transduction pathways, especially related to apoptosis, kinases and hormone receptors. At the GSR, he has been responsible for assisting clients with experimental design and execution, primary/secondary data analysis, bioinformatics, as well as developing novel scientific and bioinformatic methodologies. His role as technical director has synergized extremely well with his research program and has afforded him the opportunity to actively engage in the research programs of many investigators. Dr. Tepper runs the day-to-day scientific operations of the GSR and is available by appointment for consultation.
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Ryan Davis, B.S. (Genomics Specialist) 
Mr. Davis has been a key member of the GSR since 2002 and was asked to assume the role of lead technician at the GSR in 2004. Over the years, Mr. Davis has become one of the leading experts in genomics technologies in Northern California and is well respected by senior consultants, field application scientists and regional representatives from Affymetrix, Agilent, Illumina, and BioDiscovery. Mr. Davis also has extensive knowledge of computing and is highly skilled in the analysis of complex datasets. He is responsible for maintaining the GSR’s computer network, Linux-based computer cluster, and secure FTP server. Mr. Davis performs the majority of the laboratory services and is available by appointment for technical and logistical consultation.
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Stephenie Liu, B.A. (Manager) 
Ms. Liu has served as the GSR administrator since 2001. She has considerable experience in the genomics field, having worked with DNA sequencing and microarrays since 1996. Ms. Liu provides administrative support for interactions with Cancer Center administration, purchasing, billing, cost analysis, website supervision, grants and publication support, and development of educational seminars. In addition, she has been fully trained by applications scientists on the Affymetrix microarray and Illumina NGS platforms and assists in sample and array processing (e.g., target preparation, fluidics, scanning), as needed. Ms. Liu is available to help clients with any administrative or billing needs, and can also help to schedule consultation appointments.
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The Genomics Shared Resource is part of the UC Davis Health System in Sacramento, California.

To contact us:
Genomics Shared Resource
UC Davis Medical Center, Research III
4645 2nd Ave., Room 3200D
Sacramento, CA  95817
Laboratory: 916-703-0366
Fax: 916-703-0367
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Sample submission instructions

Submit a request:

  1. Download the appropriate service request form.
  2. Complete all required fields electronically.
  3. Email the completed form as an attachment to mpsr@ucdavis.edu.
  4. Our lab will follow up with you by email regarding your request.

If you need assistance, please contact the Genomics Shared Resource at 916-703-0366.