Cancer Functional Genomics

Core Leader: Muralidharan Jayaraman Ph.D. PMP.
Location: Stanton L. Young Biomedical Research Center (BRC) – Rm. 1401

Gene expression variability across the genome has significant impact on understanding the progress and prognosis of cancer. The Cancer Functional Genomics Core at the Stephenson Cancer Center offers cutting-edge technology that can provide extremely accurate and reliable expression data to support drug discovery research. The versatile Agilent SureScan Microarray Scanner system provides the ability to scan genome-wide microarray profiles. For quality assessment of purified RNA and DNA, there are two instruments that include the Biorad Experion™ Automated Electrophoresis Station and Agilent 2100 Bioanalyzer. The Biorad CFX96™ Touch Real-Time PCR Detection System provides highly-reliable quantitative individual gene transcription profiling. Functional analysis of proteins using biochemical assay can be evaluated with the Perkin Elmer EnVision® Multilabel Reader. An ultimate high-throughput high-content imaging instrument, Operetta from Perkin Elmer can provide high resolution images for screening drugs under live and fixed cell context. Live cell metabolic changes with respect to oxygen consumption and pH change due to respiration can be determined using Xfe 96 extracellular flux analyzer exclusively from Seahorse.

To request any service, visit the iLab page for the shared resource facility. You may need to set up your account when you visit iLab for the first time. Within iLab, you can request various services, monitor and communicate about the progress of your project.

Services

• Array Scanning and Quantification
• Reverse Proteomics Array
• Real-Time PCR
• Multimodal Assay Screening
• DNA / RNA / Protein Purity Analysis on a Chip
• High-content drug screening
• Metabolic analysis of live cells
• Absolute allele copy number determination

Equipment

• Agilent SureScan Microarray Scanner System
• Biorad CFX96™ Touch Real-Time PCR Detection System
• Perkin Elmer EnVision® Multilabel Reader
• Biorad Experion™ Automated Electrophoresis Station
• Agilent 2100 Bioanalyzer
• Arrayit Nanoprint™
• Xfe 96 extracellular flux analyzer
• Perkin Elmer Operetta
• Arrayit Spotware scanner

Contact

For more information about the Core please contact:
Muralidharan Jayaraman, Ph.D., Director of Research Core Operations.
Email: Muralidharan-jayaraman@ouhsc.edu
Phone: 405-271-8001 x30492

Equipment

Agilent SureScan Microarray Scanner System

The SureScan Microarray Scanner is a state-of-art, laser-induced fluorescence scanner designed to read microarrays printed on standard 1” × 3” slides. The SureScan scanner measures the fluorescence intensity of labeled sample nucleic acid (DNA and RNA) bound to microarrays. Data extraction is handled by the Feature extraction program available on the connected computer.

Scanner capabilities:

• Scan CGH, CGH+SNP, ChIP-on-chip, DNA methylation, microRNA arrays with dual color and up to 3 microns sensitivity
• Feature extraction software extracts data from scanned images.

Operating and Handling Procedures

Investigator designs and runs their microarray slide hybridization protocol. For hybridization of the slides, core houses a hybridization oven with adjustable temperature for investigator use.

Scheduling to scan slides on the Agilent Surescan Scanner is done with our online scheduler. Slides can be scanned by the core personnel as per the investigator protocol.

Sample quality control:

DNA and RNA samples quality of purity can be evaluated using either BioRad Experion or Agilent Bioanalyzer available in the core facility.

Data storage and retrieval:

All generated data is stored online on university server in user specific folder, which is to be set up before their first use. Local data transfer can be done using storage devices like USB stick or external hard drives.

Data analysis:

Data extraction can be done with the Feature extraction software that is provided in the accompanying computer.

Data Retention policy:

Data will be stored for 1 year from the collection date on the server. It is the investigator responsibility to store their data after this time period.

Biorad Experion™ Automated Electrophoresis Station and Agilent 2100 Bioanalyzer

The Experion Automated Electrophoresis Station performs all the steps for gel-based electrophoresis in one compact, durable unit. The Experion Automated Electrophoresis System can be used upstream and / or downstream of a number of nucleic acid- and protein-applications.

The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells.

Equipments capabilities:

• DNA / RNA / Protein purity analysis

Operating and Handling Procedures

Scheduling for the equipment can be done with our online calendar for Experion and Bioanalyzer. Individual user designs and runs their protocol, however new protocols designed are done with core personnel. All reagents and plastic wares are to be provided by the user.

Data storage and retrieval:

All generated data is stored online on the university server on user specific folder, which is to be set up before their first use. Local data transfer can be done using storage devices like USB stick or external hard drives.

Data analysis:

Data analysis is done with the Experion manager or 2100 Expert installed on their respective computers. It is also possible to export data to excel file for further analysis.

Data Retention policy:

Data will be stored for 1 year from the collection date on the server. It is the investigator responsibility to store their data after this time period.

Nanoprint Microarray Printing

Nanoprint™ Microarrayers are platforms for all microarray manufacturing applications including DNA microarrays, protein microarrays, and other types of biomolecules. Based on advanced nanotechnology, Arrayit NanoPrint™ robots move with 500 nanometer resolution and deliver sub-nanoliter sample volumes using high throughput, patented contact printing devices.

Applications include:

• Reverse Phase protein lysate microarray
• Proteomic microarray
• Antibody array
• Peptide array

Operating and Handling Procedures

Microarray printing is provided as a service to the research community. Following is the standard protocol to use this facility:

• For microarray printing, a project number will be assigned to the project, which will be discussed with the core personnel.
• Preliminary quote with pricing for the microarray printing will be provided to the researcher.
• Upon agreement on the quote, the required reagents will be procured.
• The sample to be used for printing will be evaluated following appropriate quality control protocol before printing.

Data storage and retrieval

All generated data/protocol is stored online on university server in user specific folder, which is to be set up before their first use.

Data Retention policy

Data will be stored for 1 year from the collection date on the server. It is the investigator responsibility to store their data after this time period.

XF analyzer XF^e 96

XF^e 96 Extracellular Flux Analyzers are advanced cell metabolism analyzers measuring two major energy producing pathways of the cell-mitochondrial respiration and glycolysis in a 96 well plate, in real-time. It can determine in vitro oxygen consumption, glycolysis, CO₂, mitochondrial dysfunction and fatty acid oxidation. Accompanied with the analyzer, is a Seahorse designed XF prep station to prepare your culture plates for assay. The XF prep station delivers fast, meticulous and thorough washing of your cells, ensuring consistent assay conditions.

Operating and Handling Procedures

Scheduling to work on the XFe 96 is done with our online scheduler here. Individual user designs and runs their protocol, however new protocols designed on this system are done with core personnel. All reagents and plastic wares are to be provided by the user.

Data storage and retrieval:

All generated data/protocol is stored online on university server in user specific folder, which is to be set up before their first use.

Data analysis:

Data analysis is done with the XF wave software manager installed on the system computer as well as software provided to the investigator. Also, it is possible to export data to excel file for further analysis.

Data Retention policy:

Data will be stored for 1 year from the collection date on the server. It is the investigator responsibility to store their data after this time period.

Perkin Elmer Operetta^®

Perkin Elmer Operetta^® High Content Imaging System can be used for automated image acquisition from slides to plates. Low and high magnification field view accommodates whole cell or region of interest detailed analysis. Harmony^® analysis software is well equipped to set up assays, automate experiments and analyze data. Analysis of images can be configured as building blocks. Cells can be analyzed based on their fluorescence and texture, for their intensity and morphological characteristics.

Operating and Handling Procedures

Imaging projects have to be submitted through our project submission form. Scheduling for setting up the protocol for the assay will be provided with required positive and negative controls cleared spelled out by the core personnel. After the protocol is properly set up, scheduling for experimental image analysis will be done by the core personnel.

Data storage and retrieval:

All generated data/protocol is stored online on university server in user specific folder, which is to be set up before their first use.

Data analysis:

Data analysis is done with the Harmony software manager installed on the system computer. Also, it is possible to export data to excel file for further analysis.

Data Retention policy:

Data will be stored for 1 year from the collection date on the server. It is the investigator responsibility to store their data after this time period.