gy) and 5 ml 10% SDS, heated at 95uC for 5 min and cooled to room temperature. Each sample was applied to a slide which was incubated in a water bath in the dark at 42uC for 18 hours, washed and scanned using a GenepixH 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Every hybridisation was per- formed in duplicate, and the dyes were swapped in a balanced design to counteract any possible probe-specific dye effects. Microarray data normalisation and analysis Each scanned TIF image was quantified using Genepix Pro 6.0 software (Molecular Devices) to obtain foreground and back- ground intensity values for each spot. Genepix was configured to generate the custom morphological close-open background estimator, which is less variable than the more usual local background estimators[18]. All normalization and differential expression analysis was conducted using the limma software package[19] for the R programming environment (http://www. r-project.org). A small offset was added to the intensities before background correction to ensure that there were no negative background-corrected intensities or missing log-ratios and to stabilize the variability of log-ratios in the low-intensity range. Microarray data quality was checked using diagnostic image plots and MA-plots and was found to be satisfactory. Log-ratios were print-tip loess normalised[20], ensuring that low-intensity log- ratios remained of low variability. This made it unnecessary to filter low-intensity spots from the analysis and allowed all spots to be included in the differential expression analysis. A linear model approach was used to analyse all the microarrays for the two individuals and four cell populations together. Tests of statistical significance between the three time points were conducted for each cell population using empirical Bayes moderated t-tests, which borrow information between genes and References 1. 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