Up- and down-regulated genes in Notch1-IC/EREB, Notch2-IC/EREB, and EBNA2/EREB cells. Affymetrix GeneChip analysis was performed with the human HGU133 Plus 2.0 chip. Notch1-IC/EREB, Notch2-IC/EREB, and CAT/EREB cells were induced and harvested, as outlined in Figure 1B. Before the preparation of total RNA, ΔNGFR⁺ cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline (Figure S3). As negative control, CAT/EREB cells in the absence of estrogen and presence of doxycycline were treated in the same way as Notch1/2-IC/EREB cells. To study EBNA2-regulated genes, CAT/EREB cells were induced by estrogen (EBNA2/EREB). Three independent experiments for each time point were performed to ensure a statistically relevant dataset. Only 17 probe sets were found to be differentially expressed in CAT/EREB cells, excluding a considerable background activity of the tetracycline expression system. (A) Numbers of significantly regulated genes with an at least 1.5-fold induction or repression within any point during the kinetics by Notch1-IC, Notch2-IC, or EBNA2. (B) Significantly regulated genes with an at least 1.5-fold regulation were used for compilation of Venn diagrams to depict genes regulated solely or commonly by Notch1-IC, Notch2-IC, or EBNA2.