<p>All 8 core iPSC lines were differentiated for 14 days in triplicate wells, lysed for RNA, amplified to generate cRNA, and ran on the Illumina HumanHT-12-14 BeadChip platform. <i>A</i>. Clustering of 8 core lines by correlation. UR stands for unrelated control. <i>B</i>. Scatter plot (log scale) of the correlation of gene expression between 4 control lines and 4 PSEN1 lines. The red lines indicate a 3-fold expression difference. <i>C</i>. Chart indicating the number of upregulated (shown in blue) and downregulated (shown in yellow) genes for each threshold of analysis. “DiffScore” refers to genes with a Diff Score of >13 (upregulated) or <13 (downregulated), which indicate a change in expression with a pValue of p≤0.05, without regard to the relative fold change. Criteria for fold change categories include the listed fold change as well as statistical significance. See also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084547#pone.0084547.s007" target="_blank">Table S1</a>.</p
