Genomics
The GSR serves the cancer research community with centralized, cost-effective services and comprehensive expertise in genomics and bioinformatics. Investigators have access to contemporary genomic applications and state-of-the-art instrumentation for next-generation sequencing (NGS) and spatial transcriptomics.
The GSR also provides ancillary genomics services for nucleic acid isolation, quality assessments, DNA shearing and quantitative PCR. Our unique features include:
- Complete repertoire of high-resolution genomics services
- Development of customized protocols
- Specialization in translational genomics and analysis of clinical specimens
The GSR offers hands-on specialized training, mentorship and monthly workshops to support cancer studies. We provide consultation for experimental design, project logistics and management and manuscript and grant proposal preparation. Our faculty have expertise in bioinformatics, cancer genomics, DNA sequencing and epigenomics.
Services
We provide a comprehensive suite of genomics services to support your cancer research. Grant writing support is available from all Shared Resources, including support letters, recommendation, statistical analysis, etc.
Bioinformatics and Data Analysis
The GSR’s extensive, integrative bioinformatics support ensures you receive interpretable results from your genomics studies. Our specialized computation platforms, servers and tools facilitate analyses of highly complex data sets.
We also have multiple analysis pipelines in place. The GSR possesses the capability for:
- Advanced analyses, including functional interpretation of expression signatures
- Analyses of large-scale public NGS datasets
- Application of a variety of data integration approaches
Translational Genomics Research
The GSR provides a wide range of services for the collection, preservation and molecular analysis of multiple types of clinical specimens, including:
- FFPE tumor tissue
- Saliva
- Serum
- Whole blood
We apply specialized protocols to isolate high-quality nucleic acids from challenging samples and analyze very small specimens, like needle biopsies. Our expertise with in vivo tumor models enables us to support preclinical drug studies and research on genetic mechanisms of tumorigenesis.
Customized Protocols
We support investigator-driven projects with the ability to:
- Design methods to analyze circulating tumor DNA, exosomal miRNA and viral genomes
- Develop protocols and reagents, including targeted NGS panels
- Implement laboratory-developed tests
High-Resolution Genomics
We offer single-cell RNA-seq with the 10x Genomics Chromium platform. We also provide spatial transcriptomics services on the NanoString GeoMx® Digital Spatial Profiler (DSP) and 10x Genomics Visium platforms.
[Awaiting current rate information from UCDH.] Refer to rates excel spreadsheet
Subsidized Rates for Cancer Center Members
Members of the cancer center receive priority access and subsidized rates for Shared Resources services. Not yet a member? Learn about the benefits and privileges of cancer center membership.
Our team looks forward to providing a solution for your complex genomics and bioinformatics-related research.
To request our services, please download and complete the appropriate service request form:
Email the completed form(s) as an attachment to gsr@ucdavis.edu. A member of our staff will follow up with you by email regarding your request.
NOTE: A PPMS account is required. View our quick start guide for creating an account or set up an account.
For questions about our services, please contact:
John McPherson, Ph.D. | Director: Phone: Email
Ryan Davis, B.S. | Genomics Specialist: Email
Stephenie Liu, B.A. | Manager: Email
GSR staff
To reach GSR staff, please call the laboratory at 916-703-0366 or contact us.
Fax: 916-734-2698
Location
The GSR facility is located at UC Davis Medical Center: 4645 2nd Avenue, Research III, Room 2400, Sacramento, CA 95817
Please read our policies and procedures below to ensure the GSR runs smoothly and efficiently.
By submitting samples to the GSR, the primary investigator and all researchers involved agree to the following:
- Some processes consume samples. As a result, the GSR may not return every sample you send to us. We discard remaining samples three months after notifying a client about completion of an order.
- The user must cite UC Davis Comprehensive Cancer Center Genomics Shared Resource (NCI P30 CA93373) in the acknowledgements section of any published work (manuscript, poster, presentation, etc.) that uses data obtained through work done by the GSR. The user must also notify the GSR of any potential and actual publication(s) that use data obtained through work done by the GSR. This condition of use is vital for the success of the shared resource and of UC Davis Comprehensive Cancer Center. It plays a crucial role in helping us earn a competitive renewal of the Cancer Center Support Grant and to retain our NCI designation.
- The GSR reserves the right to use any data from services performed by the GSR. We use data to assess the quality of data generated by our facility and to develop technical protocols and analysis tools. We keep all details pertaining to the data, samples and treatments confidential. The GSR will never exploit the biological relevance of a user's experiment.
- The GSR is not responsible for animal or human subject assurances pertaining to the samples submitted. By submitting samples, the user assures the GSR that they have obtained all the appropriate animal subjects or human subjects protocol approvals for their study. Users will not submit samples to the GSR unless they have met all the requirements for animal or human studies.
- We require 24-hour notice of cancellation for instrument bookings. Cancellations made less than 24 hours in advance are subject to fees. The fees will cover the GSR's costs for setting up the instrument and reserving the time slot.
- We charge for costs associated with damage to instrumentation due to user error. Charges apply to the account provided by the user at the time of instrument booking.
RNA Protocols
We recommend the following protocols for isolation of high-quality RNA for use in RNA-Seq and small RNA-Seq library preparations:
Explore helpful resources on working with RNA, which include how to assess RNA quality and maintain an RNase-free lab.
NOTICE TO ALL NIH-FUNDED INVESTIGATORS
CCSG Acknowledgement: research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number P30CA093373. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
GSR Acknowledgement: the authors wish to acknowledge the support of the UC Davis Comprehensive Cancer Center Genomics Shared Resource, supported by the National Cancer Institute of the National Institutes of Health under award number P30CA093373. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
This resource is funded by the Cancer Center Support Grant (CCSG) awarded by the National Cancer Institute (NCI P30CA093373). Publications that have utilized facility resources, services or scientific data generated by the resource should acknowledge the resource or the assistance provided by resource staff and cite the NCI CCSG. An electronic copy of the publication should also be sent to the resource directors.