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. We regularly prepare sequencing libraries for RNA-seq, whole exome, whole genome, ChIP-seq, Hi-C, CUT&RUN, single-cell transcriptomics, spatial transcriptomics, spatial proteomics, and a variety of other NGS applications.
The GSR also provides ancillary genomic services for nucleic acid isolation, quality assessments, DNA shearing, and quantitative PCR. Our unique features include:
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.
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.
The GSR provides comprehensive support for genomic research, specializing in RNA-seq, whole-exome sequencing (WES), whole-genome sequencing (WGS), and ChIP-seq analysis. We assist researchers with library preparation, quality control, and bioinformatics, enabling insights into gene expression, genetic variation, and epigenetic regulation.
Our team offers expert consultation and customized data analysis to ensure high-quality, reproducible results. Whether studying human health, model organisms, or non-model species, we tailor our services to meet diverse research needs, helping scientists extract meaningful insights from complex genomic data.
We offer cutting-edge single-cell RNA sequencing (scRNA-seq) and spatial biology services to explore gene expression at unprecedented resolution. Using the 10x Genomics Chromium platform, we provide high-throughput single-cell transcriptomics, enabling researchers to study cellular heterogeneity and dynamic gene expression in complex tissues.
For spatial biology, we support NanoString GeoMx Digital Spatial Profiling and 10x Genomics Visium, allowing precise.
The GSR provides a wide range of services for the collection, preservation and molecular analysis of multiple types of clinical specimens, including:
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.
We support investigator-driven projects with the ability to develop protocols for specialized genomics applications, including:
The GSR provides comprehensive bioinformatics support, ensuring that your genomics data is both interpretable and actionable. Our specialized computational infrastructure, including high-performance servers and advanced analytical tools, enables the processing of complex datasets with efficiency and precision.
We offer a range of customized analysis pipelines, including:
With our expertise, you can confidently extract meaningful biological insights from your genomics research.
Below are the rates for a sampling of the GSR's most commonly requested services. For genomics services not listed here, please contact the GSR. Please note that some services have a complex pricing structure and require project consultation in order to determine accurate pricing.
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:
Director
Email: jdmcpherson@ucdavis.edu
Genomics Specialist
Email: jdmcpherson@ucdavis.edu
Manager
Email: sliu@ucdavis.edu
To reach GSR staff, please call the laboratory at 916-703-0366 or contact us.
Fax: 916-734-2698
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:
Cell harvesting
Flash-frozen tissue collection
Always use clean, nuclease-free tools and tubes, and avoid cross-contamination between samples. Immediately after tissue harvest, dissect out a desired piece no larger than 4mm x 4mm x 4mm (for fatty tissues, cartilage, tendon, ligament, bone, or eye, contact the GSR for special instructions). Remove any excess blood and necrotic tissue. Carefully place the tissue piece on the sidewall of a microfuge tube or cryovial and snap-freeze in liquid nitrogen. Store at -80°C. Transport on dry ice only.
FFPE tissue
FFPE scrolls should be provided in 2mL microfuge tubes. Sections should be cut fresh and stored at -20°C, preferably no longer than a week. For guidance on the quantity of scrolls for various applications, please contact the GSR.
Blood collection
Saliva collection
Collect saliva using an appropriate kit from DNA Genotek (Oragene).
RNA isolation
For RNA from flash-frozen tissue, we highly recommend following our Combined TRIzol-RNeasy method <attached PDF>. For RNA from cells and other sources, we strongly recommend QIAGEN RNA isolation kits. For all RNA isolations, we require that the samples be DNased, preferably using an on-column DNase protocol.
DNA isolation
We recommend QIAGEN DNA isolation kits and require that an RNase A step be included during isolation.
Sample 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 (award number P30CA093373). Disclaimer: 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 consultation, or that include scientific data generated by the resource should acknowledge the resource and 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.