On a single BeadChip, six arrays were run in parallel as described in [14]. Each of the two IVT reactions from the 726 samples was hybridized to one array each, so that each cell line had two replicate hybridizations. cRNA was hybridized to arrays, and subsequently labelled with Cy3-streptavidin [Amersham Biosciences, Little Chalfont, United Kingdom, as described in 14] and scanned with a Bead Station (Illumina) as previously described in Stranger et al. (2005). Samples were processed in an order randomized with respect to population of origin and IVT batch.
