Detection of critical steps in the ChIP-Chip protocol. A Ratios of ChIP DNA purified with spin column versus column free purified DNA detected by qPCR for the indicated gene regions. B qPCR ratios of crosslinked-reversed versus non crosslinked DNA for indicated gene regions. C Crosslinked-reversed versus non crosslinked DNA as shown in B was differentially labeled and hybridized to a microarray. Log2 ratios are shown in blue (only values below -0.5) in comparison to the SeqA ChIP signal (from Fig. 2).