FIG. 2.

ChIP-chip data for the feaR-feaB-tynA region of the E. coli chromosome. For the ChIP-chip experiments, cultures were grown anaerobically in the presence and absence of nitrate. In the absence of nitrate, NsrR binding sites should be occupied. In the presence of nitrate, some NO is generated as a by-product of nitrite respiration, and the NsrR regulon is derepressed (5), indicating that NsrR binding sites are vacant under these conditions. After ChIP, the two samples were labeled (with Cy5 and Cy3) and hybridized together to a high-density microarray. High fluorescence ratios therefore indicate the presence of NsrR binding sites, where binding is sensitive to the presence of nitrate in culture medium. Full technical details of this experiment have been published previously (10). The data shown are the mean fluorescence ratios from three experiments, with each of the three data sets centered on a mean ratio of 1 prior to averaging. The coordinates are for a noncurrent version of the E. coli MG1655 genome sequence (http://genolist.pasteur.fr/Colibri/).