Additional data file 1.

(a) MvA plots. From left to right: MvA plots derived from high density oligonucleotide arrays to define gene expression profiles from control (C_1-3.CEL files) and TIA-1 (1_1-3.CEL files), TIAR (R_1-3.CEL files) or TIA-1 plus TIAR (1+R_1-3.CEL files)-depleted HeLa cells. This kind of plot is used to diagnose experimental problems between different biological replicates. The ratio between array signal intensities is illustrated on the y-axis (M) and intensity average is represented on the x-axis (A). In this type of plot, if there are no systematic differences between biological replicates, the dot map of each array is concentrated on the axis M = 0. In all cases documented in our experiments, there was no a significant variability between different biological samples. (b) RNA digestion plots. RNA degradation mainly started from the 5'-end and, therefore, a greater loss of signal intensity occurred with the probes that hybridize to the mRNA 5'-end than with complementary probes close to the mRNA 3'-end. RNA degradation plots illustrate mRNA intensity values versus the function of the positions corresponding to the probes in the 5'-3' orientation. Each graphic on the plot illustrates one array and the slope indicates the RNA degradation level corresponding to each hybridized sample. Overall, a higher slope indicates that more hybridized sample was degraded. This kind of plot is likely to detect significant differences between hybridized samples. Our results show that all samples behaved similarly, suggesting that there are no significant differences between biological samples analyzed. (c) Box plots of crude (to the left) and normalized (to the right) data analyzed by the quantile technique. The Data_rma.txt file submitted to the ArrayExpress database contains processed data using the Robust Multichip Average method [28]. Every color indicates a characteristic group of biological samples analyzed.

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Reyes et al. Genome Biology 2009 10:R87   doi:10.1186/gb-2009-10-8-r87