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Quantitative Gene Expression (High-Throughput)

A variety of high-throughput quantitative pcr methods are available. They are used to validate large microarray datasets or to screen gene expression patterns for specific pathways. They present a cost savings over hand-pipetted methods for projects with The Genome Core can run most varieties of plate-based high-throughput gene expression arrays.

TaqMan Arrays (384-Well Micro Fluidic Cards)

Description
The TaqMan Array is a 384-well micro fluidic card that enables a researcher to perform 384 simultaneous real-time PCR reactions without the need to use liquid-handling robots or multichannel pipettors to fill the card. This medium-throughput micro fluidic card allows for 1-8 samples to be run in parallel against 12-384 TaqMan Gene Expression Assay targets that are pre-loaded into each of the wells on the card. The Taqman array is available in various “Gene Signature Arrays” or is fully customizable with the genes of your choice. The Core possesses a special centrifuge required to spin down the arrays which is available to users.

Science
See information from Applied Biosystems.

Protocol
Users should consult the Applied Biosystems User’s Bulletin for protocols. The arrays are very simple to load, but the protocol should be read carefully so as to avoid costly errors.

Pricing
An instrument fee will be charged for each TLDA run by individual users. The machine must be reserved with the Core staff at least two days in advance of desired run. The Core staff will schedule the first available time. The Core can also load the TLDAs and the user will be charged for the time required. Please contact the Core staff about pricing.

What to Provide
Please contact the Core staff for more information. If the Core will be loading the arrays, users should provide cDNA at recommended concentrations, the recommended quantity of Applied Biosystems 2X Universal Master Mix, and the plates.

SABiosciences/Qiagen PCR Arrays

Description
Arrays using Sybr green technology are also available. These arrays may provide a cost savings for large studies, especially using the pre-designed gene pathways. Each 96-well or 384-well plate includes SYBR Green-optimized primer assays for a researched panel of relevant, pathway- or disease-focused genes. PCR Arrays can also be customized to contain a panel of genes tailored to specific research interests. Users must use the specific master mix and reverse transcription kit from SABiosciences for best results with the plates. The high-quality primer design and master mix formulation enable the PCR Array to amplify 96 or 384 different gene-specific products simultaneously under uniform cycling conditions. (reference). Plates can be run on the Core equipment and instrument times will be charged per run. Conversely, for added technician time the Core will load and run the plates for users.

Science
SYBR Green I dye intercalates into double-stranded DNA and produces a fluorescent signal. The intensity of the signal is proportional to the amount of dsDNA present in the reaction. Therefore, at each step of the PCR reaction, the signal intensity increases as the amount of product increases. For information specific to this product, go to SuperArray.com

Protocol
See information from SABiosciences.

Pricing
Regular instrument charges will be assessed. We recommend the use of the 384-well format plates, as this will provide users with the best price per run. If the Core is requested to run the plates, technician and reagent charges will be applied. Please contact the Core Staff for more information.

What to Provide
If the Core will be loading the arrays, users should provide RNA at recommended concentrations and the plates. The Core provides the reverse transcription kit and the recommended master mix. Please contact the Core Staff for more information.

Additional Resources
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.