Gene Expression Services with Commercial and Custom-made Microarrays in UC Riverside Core Instrumentation Facility
Data Analysis
New (as of June 2006)! We recently acquired a single site license for, and we now offer training in use of, ArrayAssist 4.1.1, a complete data mining and statistical analysis tool from Stratagene that is especially suited for handling .cel files from Affymetrix GeneChip scans. This software package incorporates all of the commonly used preprocessing algorithms, including RMA, GC-RMA, PLIER (and PLIER+16 for variance stabilization), Li-Wong (MBEI) and Affymetrix's MAS5. We find it to be very easy to use; and it's fast!
Affymetrix GeneChip® Capabilities
UCR CIF has complete capability in processing commercial GeneChips® from Affymetrix. The equipment includes a Hybridization Oven 640, Fluidics Station 450 and Scanner 3000, upgraded for scanning high-density tiling GeneChips®. When bringing RNAs to CIF for GeneChip® analysis, please use our RNA Submission Form. For our current "full service" and "hybridization only" charges, see Rates.
Custom Microarray Making Capabilities
UCR CIF has state-of-the-art array making capabilities in the Bio-Rad (formerly Virtek) Versarray ChipWriter Pro (Bio-Rad Laboratories). This instrument uses quill-type pins (Telechem International, ArrayIt Division) held in a 48-place holder and is capable of producing arrays of cDNAs, PCR products or oligonucleotides on aminosilane- or epoxysilane-coated microscope slides. Our SMP 2.5 pins have an uptake volume of 0.25 microliter and spot 0.6 nanoliter in 85 micron spots, for up to 215 spots per dip. Up to 49,000 spots and 100 micron spacing can spotted onto a 1" x 3" slide. A variety of other pins are available from Telechem and can be used with our instrument.The instrument accepts either 96- or 384-well source plates for cDNAs or oligonucleotides and has a stacker with maximum capacity of 32 plates for unattended operation.
CIF personnel (Yoon Gi Choi) provide orientation and training on the ChipWriter. UCR investigators pay a nominal charge for use of the instrument and pins (Rates).
This instrument also has gridding, rearraying and colony picking functions. However, these activities in CIF are currently handled by our Genetix QPIX.The QPIX is used primarily for automated colony picking, but in addition, it is used for macroarray making in printing DNAs onto nylon membranes.
Details on microarray and macroarray production and use of commercial arrays (Affymetrix GeneChips®) can be found under Services. A protocol for printing, preparing labeled cDNAs and doing the hybridizations has kindly been contributed by Heather Sanders, a UCR graduate student in microbiology: Microarray Protocols. This protocol uses "Tyramide Signal Amplification" in labeling targets, and reagents are available in kit form from PerkinElmer (Micromax TSA information and manual can be found at PerkinElmer web site).
A PowerPoint presenentation from a CIF workshop on commercial and custom spotted microarrays is available for download at: