Figure 2

ChIP-seq analysis of SOX2 in GBM cells. Quantitative real time PCR for the confirmation of ChIP-seq peaks. Relative amount of PCR products from SOX2-ChIP and IgG-ChIP were shown as bar graph with the amount of IgG-ChIP normalized to 1. Standard deviations were also shown for SOX2-IP. (B) Histograms of SOX2 binding sites around annotated TSS (Transcription start sites) Frequencies of SOX2 island binding were calculated every 10 kilobases (Y-axis). Relative distance to TSS is shown in X-axis, Negative and positive values indicate localization 5' or 3' to TSS respectively. (C). A VENN diagram showing the overlaps of SOX2 targets among human GBM cells, human ES cells and mouse ES cells. (D). The consensus sequence wwTGnwTw with log-likelihood score of 13920.71 identified by the MotifSampler program. The over represented sequences were used as input for the Weblog program (http://weblogo.berkeley.edu/) [53] to display the consensus sequence graphically.