biogem

Sentrix® Expression BeadChips

Services

The Biomedical Genomics Facility is fully equipped to process the Illumina Sentrix® Expression BeadChips, once total RNA has been provided by the investigator. Equipment in the Facility include the Illumina BeadStation 500 Scanner and the ancillary equipment needed for processing Illumina arrays.

At present we offer direct hybridization gene expression services using whole genome and focused array content.

Researchers have the option of providing BIOGEM with total RNA or performing their own target labeling after which BIOGEM will hybridize and scan their slides. For optimal microarray data generation, researchers are encouraged to have BIOGEM perform the labeling and hybridization.

Illumina is currently providing BIOGEM with special pricing for biochips and the requisite reagents.

Researchers interested in this platform are encouraged to contact Chad D. Geringer at Illumina for additional information about special promotions and updates.

Chad D. Geringer (Illumina)
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121-1975
Tel: 858-201-9695(c)
email: cgeringer@Illumina.com
Web: www.illumina.com
www.switchtoi.com

Running a Sentrix® Expression BeadChips experiment at BIOGEM

Read the detailed instructions on the options for running Illumina biochip experiments at BIOGEM and fill out the online form. RNA must be resuspended with RNAse-free water (NOT DEPC WATER) at a concentration of 1 mg/ml, concs less than this will incur an extra charge if we have to concentrate the material. Please let us know in advance if the RNA is not at 1 mg/ml. Illumina is a one-color platform, meaning that the researcher can run one sample per array. Please order Sentrix® Expression BeadChips from Chad D. Geringer and have the slides shipped directly to James Sprague.

Sample and Sentrix® Expression BeadChips submission can be done once the online form has been filled out. Please co-ordinate with James Sprague for sample drop off. All RNA samples for target labeling or labeled cRNA targets must be submitted on dry ice. BIOGEM will label total RNA according to Illumina labeling protocol.

RNA and aRNA for use with Illumina Sentrix® Expression BeadChips will be subjected to a QC step in the Bioanalyzer will be used to assess the quality of the RNA. Total RNA provided by the investigator will be assessed for its suitability for labeling and subsequent hybridization. There is a 10$ charge per total RNA sample. Additionally post labeling, the biotin-UTP labeled cRNA targets will be assessed for their suitability for hybridization to Illumina Sentrix® Expression BeadChips. There is an additional 10$ charge per cRNA sample. If the target does not meet the BIOGEM quality standards the labeling will be repeated. For investigators providing labeled cRNA targets that are suboptimal the experiment will be halted and the user will be notified.

Once the Sentrix® Expression BeadChips have been processed i.e. (hybridized and washed), they will be scanned according to Illumina specifications and the resulting image files and data analysis files will be deposited on the BIOGEM SUN server. A user account will be created for the researchers to allow access to their data. This data will be only be accessible by the researcher and will not be visible to other researchers. The quality of the hybridizations and overall experimental performance are determined by a visual inspection of the raw scanned data. BIOGEM will generate a Project Report, which will include a summary of the particular experiment, RNA and cRNA quality data, labeling data, the hybridization log, scans, and feature extracted data. All data files are backed-up from the server to an off site location routinely. Currently, BIOGEM slide hybridization services include quantifying of the slide images using Illumina's BeadArray software and export of the data for use with many analysis programs (e.g. GeneSpring, GeneSight, GeneLinker Gold, D-Chip, Spotfire etc). Gene ontology and pathway analyses are carried out on the data.

Researchers desiring additional help with data analysis on a fee for services basis can obtain support for analysis of their Illumina data through the BIOGEM Core (BIOGEM@ucsd.edu).

Please note the following BIOGEM Policy for Sentrix® Expression BeadChips hybridizations: The Investigator agrees that they solely are responsible for the quality of the RNA submitted. They are required to provide BIOGEM with the concentration of the sample and the OD260/280 ratio as outlined exactly on the submission page. Dilute RNA samples will incur an extra charge. All samples will be delivered to the facility on dry ice only after coordinating a suitable drop off time with James Sprague.

To reduce the rate of failed target preparation and hybridization experiments in cRNA targets will not be prepared until RNA integrity has been established. BIOGEM is not responsible for replacing slides when the Quality Controls for the hybridization are valid. Furthermore, BIOGEM is not responsible for the quality of the data when the investigator supplies the labeled cRNA.

Last Updated March 2008
By Dr. Gary Hardiman