Figure 6.

Comparing mock IP experiments generated by different antibodies from fly embryos. The spurious binding sites were detected from the IgG antibody mock IP, GFP antibody mock IP, and ACF1 antibody mock IP using their corresponding DNA input controls. The consistency between the two sets of spurious sites is indicated by the number of overlapped sites divided by the number of total sites (A). Compared to the DNA input, the IgG antibody mock IP, and ACF1 antibody mock IP, the GFP antibody mock IPs predicted much fewer binding sites from ChIP-seq (B), and the resulting binding sites contained more target motifs (C). The whiskers in panel C indicate the standard errors of the means of motif fractions. The samples sizes are 127 and 44 respectively for fly and worm.