Overview of the microarray expression data. A. Design of the experiment. This study includes 30 hybridizations using cDNA arrays (ArrayExpress accession numbers A-MEXP-175 and E-MEXP-431). Fourteen slides were allocated for profiling each of the DoxHPC1 and DoxHPC7 lines. Technical replicates were included at three different levels (replicated cell cultures of both cell lines, replicated hybridizations in each comparison using reciprocal dye assignments and repeated measurements using probes printed twice on each array). The hybridization scheme also includes two hybridizations between the two cultures within each cell line, as well as two hybridizations between the different Lhx2-expressing cell lines. The 36, 72 and 96 hours refer to the time after Lhx2 expression was down-regulated through withdrawal of dox from the culture medium. Each arrow denotes one hybridization. The tip and the base of the arrow indicate Cy5 and Cy3 assignments of the dyes, respectively. Letter assignments by the arrows (A, B, C and D) are used to describe the comparisons in the text. Figure C, D and E show the MA-plots for the comparisons at 36 (A), 72 (B) and 96 hours (C) respectively. Figure B, F-H show the statistical significance (1 - log of p-value) for each probe to be differentially expressed versus the M-value in a volcano-shaped plot; B between the cell lines DoxHPC1 and DoxHPC7 in E-comparison at time 0 hours and F-H corresponding values for the A-C comparison. Differentially expressed genes are shown in red. The feature corresponding to Lhx2 is indicated with an arrow.