Because CIDR hoped to determine if the Affymetrix 10k assay could be used to quickly genotype large numbers of samples, standard Affymetrix 10k protocols were adapted in collaboration with Affymetrix to include automation for all liquid handling steps in a 96-well plate format. Barcode tracking was used to assign plate and well positions to specific Affymetrix GeneChips. Standard Affymetrix protocols were used for chip handling, scanning, and data analysis.
