6
David Weaver et al.
Fig. 1 Representative absorption spectrum of a good-quality RNA sample
Several cDNA preparation kits are available from commercial vendors such as Bio-Rad, Life Technologies, and QIAGEN. 3. Use the RNA for preparation for Affymetrix arrays: In this case, Affymetrix has a unique procedure for one-cycle cDNA synthesis, target labeling, and cRNA preparations. Follow the Affymetrix manual, which is quite detailed and self-explanatory for the most part. Please note that besides Affymetrix, there are a number of additional commercial microarray service providers for your hybridization experiments (Table 1). 2.13 Microarray Hybridization, Washing and Staining of Sample Targets
For experiments described in our work [9], we used the Affymetrix GeneChip® microarrays (http://www.affymetrix.com/estore/). The Affymetrix system used consisted of the Affymetrix GeneChip® Hybridization Oven 640, the Affymetrix GeneChip® Fluidics Station 450, and the Affymetrix GeneChip® Scanner 3000 6G. The software utilized was the Affymetrix GeneChip® Operating Software (GCOS), version 1.4. Manuals used for protocols were the GeneChip® Expression Analysis Technical Manual (catalog number 702232, Revision 3) (http://media.affymetrix.com/ support/downloads/manuals/expression_analysis_manual.pdf) and the GeneChip® Expression, Wash, Stain and Scan User Manual (catalog number 702731, Revision 3) (http://media.affymetrix. com/support/downloads/manuals/wash_stain_scan_cartridge_ arrays_manual.pdf). For user-prepared protocols, in the Analysis
