A. Summary of binding data for Oct4, Sox2, Nanog and Tcf3. 14,230 sites are co-bound genome wide and mapped to either promoter proximal (TSS +/− 8kb, dark green, 27% of binding sites), genic (>8kb from TSS, middle green, 30% of binding sites), or intergenic (light green, 43% of binding sites). The promoter proximal binding sites are associated with 3,289 genes. B. (upper) Binding of Oct4 (blue), Sox2 (purple), Nanog (orange) and Tcf3 (red) across 37.5kb of mouse chromosome 3 surrounding the Sox2 gene (black box below the graph, arrow indicates transcription start site). Short sequences uniquely and perfectly mapping to the genome were extended to 200bp (maximum fragment length) and scored in 25bp bins. The score of the bins were then normalized to the total number of reads mapped. Oct4/Sox2 DNA binding motifs (Loh et al., 2006) were mapped across the genome and are shown as grey boxes below the graph. Height of the box reflects the quality of the motif. (lower) Detailed analysis of three enriched regions (Chromosome 3: 4,837,600-34,838,300, 34,845,300-34,846,000, and 34,859,900–34,860,500) at the Sox2 gene indicated with dotted boxes above. The 5’ most base from ChIP-seq were separated by strand and binned into 25bp regions. Sense (darker tone) and anti-sense (light tone) of each of the four factors tested are directed towards the binding site, which in each case occurs at a high-confidence Oct/Sox2 DNA binding motif indicated below.