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Differential expression of OCT4 and NANOG targets in RNAi experiments
| Method for determining bound targets | Percent of differentially expressed OCT4 targets on OCT4 knockdown | Percent of differentially expressed NANOG targets on NANOG knockdown |
| ChIP-chip only | 33.9% (390/1,151) | 21.4% (192/898) |
| ChIP-PET only | 29% (114/393) | 14.8% (91/616) |
| ChIP-chip + ChIP-PET | 70.3% (83/118) | 33.5% (73/218) |
| Percent of regulated genes | ||
| Upregulated | 39.4% | 50.6% |
| Downregulated | 60.6% | 49.4% |
