Cancer Institute A national cancer institute
designated cancer center

Genomics Shared Resource


http://microarray.org
http://cmgm.stanford.edu/pan
http://mendel.stanford.edu/ssc/

Facility Director: John Coller, PhD
Facility Co-director: Michael Eckart, PhD
Faculty Advisor: Pat Brown, MD, PhD
Faculty Co-advisor: Arend Sidow, PhD

Contact

John Coller, PhD (main contact)
Director, Genomics Shared Resource
Director, Stanford Functional Genomics Facility
Rm 0120, CCSR Building
Stanford, CA 94305
(650) 736-1026
E-mail: john.coller@stanford.edu

Ziming Weng, PhD
Sequencing Service Center
R301 Edwards Building
Stanford, CA 94305
(650)- 724-3023
Email: zweng@stanford.edu

Michael Eckart, PhD
Co-director, Genomics Shared Resource
Director, Protein and Nucleic Acid Facility
279 Campus Drive West
Beckman Center, Rm B065 or B017
Stanford, CA 94305
(650) 723-1907
E-mail: meckart@stanford.edu

Overview

The Genomics Shared Resource (GSR) is a state-of-the-art genomics facility dedicated to providing the latest genomic research tools at low-cost. The primary goal of the GSR is to facilitate high-impact genomic-based cancer research by Stanford Cancer Center members. This goal is accomplished by providing Cancer Center members with access to cutting-edge technologies and providing the services, expertise, and scientific support necessary for utilizing these genomic tools. Technologies and services currently provided by the GSR include: high-throughput sequencing (Illumina Genome Analyzer II, ABI SOLiD, Roche Genome Sequencer FLX, and Helicos HeliScope), microarray services utilizing Affymetrix, Agilent, Illumina, Nimblegen, Stanford, and other platforms, genotyping services utilizing the Affymetrix and Illumina platforms, real-time quantitative PCR. Genomic reagents, such as clones, microarrays, and spike-in controls, are also provided. Expert assistance with the use of these technologies is also provided throughout the entire experimental process. Guidance with experimental design, data analysis, data archiving, and publication is a major component of the GSR. The resources of the Stanford Functional Genomics Facility (SFGF), Protein and Nucleic Acid Facility (PAN), and Stanford Microarray Database (SMD) have combined to provide the full spectrum of services offered by the Genomics Shared Resource and has a total combined operating budget of $3M. John Coller, PhD (SFGF), is the Director of the shared resource, and Catherine Ball, PhD (SMD) co-directs the GSR. Patrick Brown, MD, PhD, and Gavin Sherlock, PhD, are faculty advisors. There are currently 96 Cancer Center members using the shared resource, representing all program affiliations. In 2008, Cancer Center members published 39 papers using data stored and analyzed using the Stanford Microarray Database component of the GSR. Future goals are to increase access to high-throughput sequencing technologies and improve bioinformatics support and infrastructure required to implement the latest generation of genomics tools.

Services


Microarray Production

The GSR maintains a fully equipped microarray production clean room facility and can produce microarrays of any type of biological material (cDNAs, oligonucleotides, antibodies, proteins, peptide, carbohydrates, cells or cell lysates, etc). Currently, the facility offers pre-printed whole genome Human (Human Exon Evidenced Based Oligonucleotide, HEEBO) and Mouse (Human Exon Evidenced Based Oligonucleotide, MEEBO) oligonucleotide microarrays, human, mouse, and rat miRNA microarrays, and an assortment of cDNA arrays. Additionally, the GSR provides custom microarrays for Cancer Center members utilizing a large and diverse number of biological materials. Examples include a live cell microarray for the investigation and discovery of cancer stem cell biomarkers and an antigen microarray for epidemiological surveillance. These custom spotted microarrays, which are currently being developed in collaboration with Cancer Center members, hope to advance our understanding of how antigen interactions contribute to the initiation and persistence of cancer.

Microarray Processing

The GSR has considerable experience and expertise with most microarray platforms and offers a complete service utilizing Affymetrix, Agilent, Illumina, Nimblgen, Stanford and other commercial and custom arrays.  All scientific applications utilizing these platforms are available, including gene expression profiling, miRNA expression profiling, DNA methylation, array comparative genomic hybridization (aCGH), chromatin immunoprecipitation followed by microarray analysis (ChIP-chip), and SNP genotyping.  Each of these microarray applications have advanced our knowledge of the biological mechanisms involved in oncogenesis, as well as provide insights into the diagnosis, prognosis, treatment, and prevention of cancer.  In the future, these technologies will continue to play an important role in cancer research.

The Genomics Shared Resource is equipped with complete state-of-the-art Affymetrix GeneChip and Illumina BeadArray Systems. These platforms are currently provided as a full service option for all users of the shared resource. The resource also has state-of-the-art equipment for processing Agilent, Nimblegen, Stanford, and all microscope slide based microarrays. Full service for these microarray platforms is offered as well as an option for scientists to use the equipment on a 24/7 basis to perform their own experiments. This option is quite attractive for investigators wishing to minimize the costs associated with these technologies. Assistance and training is provided to all Cancer Center members who require help in using the equipment or microarray platforms offered.

High-throughput Sequencing

A recently added service to the Genomics Shared Resource is high-throughput sequencing. Currently the facility operates one Illumina Genome Analyzer II and funding is in place for acquiring a second high-throughput sequencer later this year. In addition, the GSR also provides Cancer Center members access to the other high-throughput sequencers currently located on the Stanford School of Medicine campus. The machines currently accessible include two (2) Roche Genome Sequencer FLXs, two (2) ABI SOLiDs, one (1) Helicos HeliScope, and five (5) Illumina Genome Analyzer IIs.

Doping Controls and Clones

The Genomics Shared Resource has developed a set of 169 RNA spike-in controls from Methanocaldococcus jannaschii for microarray, quantitative PCR, and sequencing applications. Thirty of these controls have been chosen for inclusion in the RNA spike-ins controls currently being produced and tested by the External RNA Controls Consortium (ERCC). The controls range from 125bp to 8000bp in length. The GSR makes these controls available to all Cancer Center members for a nominal fee. The controls can be ordered as a premixed set or individually. These controls currently play an important part in quality control for microarray experiments and will be used as standards for qPCR and high-throughput sequencing reactions.

The GSR also provides Open Biosystems reagents to the Stanford research community at reduced costs. Though a negotiated agreement between SFGF and Open Biosystems, Cancer Center members receive a 25% discount over the list price and free shipping. On average, this service has saved Cancer Center members over $25,000/year since its inception two years ago.

Microarray Analysis and Data Management

The GSR provides researchers with all necessary bioinformatics support for microarray experiments. This includes data analysis, data sharing, and secure data storage, the bulk of which is done through the Stanford Microarray Database (SMD). SMD is a relational Oracle database that stores data from many microarray platforms and provides the biological annotation, quality assessment tools, data analysis methods, visualization tools, and publication tools required for clinical research using DNA microarrays. The database and software packages are being actively developed to keep abreast of new applications of microarray technology and new data analysis methods. The package provides multiple methods for microarray data normalization (e.g., Lowess and global normalizations) and for data analysis, including hierarchical clustering, self-organizing maps, Singular Value Decomposition, and KNN-Impute for estimating missing data. Also supported are “non-expression” applications of microarrays, including array-based comparative genome hybridization (aCGH) and array-based chromatin immunoprecipitation (ChIP-chip). A key advantage of SMD is the web-based access for retrieving, annotating, data sharing, evaluating, analyzing, and publishing DNA microarray data. The GSR also makes high performance computers and many commercial software packages available free of charge to Cancer Center members. Current software packages include: DNA Analytics 4.0 (Agilent Technologies), GeneSpring GX 7.3 and 10 (Agilent Technologies), GenePix Pro 4, 5, and 6 (Molecular Devices), GenomeStudio (Illumina), Ingenuity Pathways Analysis (Ingenuity Systems), and Matlab (Mathworks).

Equipment

Access to the majority of scientific instruments housed within the Genomics Shared Resource is available to members of the Cancer Center 24 hours a day, 7 days a week (24/7).  Equipment currently available include Agilent 2100 Bioanalyzer, Agilent microarray scanner (G2565CA), ABI real-time PCR system (7900HT), 3 Axon microarray scanners (4000A, 4000B, 4200AL), Biomicro/Nimblegen Maui 12 bay Hybridization System, 2 GE Typhoons (4200 and TRIO+), Licor Odyssey Infrared Imaging System, 4 MJ Research QUAD PCR cyclers (PTC-225), Nanodrop ND-1000 Spectrophotometer, Strategene RT-PCR machine (Mx3000P), and numerous hybridization ovens, centrifuges, and other standard laboratory equipment.  Temporary bench space is also available to Cancer Center members who request it.  Assistance with the use of equipment and instrumentation is also provided during normal working hours, 8AM to 6PM Monday through Friday.  The GSR also makes high performance computers and many commercial software packages available free of charge to users of the facility.       

Operation

The Genomics Shared Resource is in the Center for Clinical Sciences (CCSR) building with additional space in the Beckman Center and Grant Buildings. Access to the CCSR facility is provided 24 hours/day, 7 days/week.  Any member of the Stanford community may request access on a 24/7 basis to the facility after creating a facility web account.  Once access is approved, researchers may enter the facility between the hours of 6 pm to 8 am Monday through Friday and on the weekends with their Stanford University-issued RFID card key. 

Access to the bioinformatics resources within the GSR is provided by through network or web-based infrastructure. The Stanford Microarray Database (SMD) provides a web-based interface for depositing, retrieving or analyzing data, publishing data sets, and collaborative sharing of the data. Any investigator on campus is welcome to use SMD and its resources for a modest charge to enable cost recovery. In addition to access to the database, access to a number of commercial software packages is provided through network license keys.

Procedures

Access to services is provided on a first-come, first-served basis. Requests for services are placed on the websites for the GSR. Normally, a meeting to go over the experimental details with the investigator is set up prior to beginning work on any research project.

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