Agilent Oligonucleotide Microarrays
The Biomedical Genomics Facility is fully equipped to process Agilent oligonucleotide arrays, once total RNA has been provided by the investigator. Equipment in the Facility includes an Agilent Scanner, and an Agilent Hybridization Oven. 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. PLEASE NOTE BIOGEM DOES NOT SUPPORT THE HIGH DENSITY FORMAT ARRAYS FROM AGILENT. THE FACILITY SUPPORTS THE 8 X 15 and 4 X 44 ARRAY PRODUCTS
Agilent is currently providing UCSD researchers with special introductory pricing for both catalog and custom arrays and the requisite reagents. Current pricing information can be obtained by contacting Sharon Henne.
Researchers interested in this platform are encouraged to contact Sharon Henne at Agilent for additional information about special promotions and updates.
Running an Agilent Experiment at BIOGEM
- Read the detailed instructions on the options for running Agilent oligonucleotide microarray experiments at BIOGEM and fill out the online form. RNA must be resuspended with RNAse-free water (NOT DEPC WATER) at a concentration of 50 ug/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 50 ug/ml. Agilent is a two-color platform, meaning that the researcher can run two samples on one array (i.e. a test and a control). Slides can be ordered directly from Agilent and shipped to Mila Angert at BIOGEM.
- Sample and Slide Submission can be done once the online form has been filled out. Please co-ordinate with Mila Angert 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 Agilent labeling protocol specified by the investigator (i.e. fluorescent direct or low RNA input).
- RNA and aRNA for use with Agilent oligonucleotide arrays 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. 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 stopped and the user will be notified.
- Once the slides have been processed i.e. (hybridized and washed), they will be scanned according to Agilent 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 Agilent's Feature Extraction software. We also provide pathway and gene ontology terms analyses.
- Researchers desiring help with data analysis on a fee for services basis can obtain support for analysis of their Agilent data through the BIOGEM Core Roman Sasik.
Please note the following BIOGEM Policy for Agilent array 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 in the online form. 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 Mila Angert.
To reduce the rate of failed target preparation and hybridization experiments in cRNA targets will not be prepared until RNA integrity has been established. If the investigator is providing cRNA, hybridization experiments will not be carried out until the cRNA 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 or cDNA target.
Last Updated June 2013
By Dr. Kristen Jepsen