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We verified these predictions by performing a ChAP-chip experiment using the Nimblegen promoter microarray.
To begin to address these questions, we have performed ChAP-chip using ENCODE and promoter microarrays.
We developed a modified ChIP-chip method, designated ChAP-chip (Chromatin Affinity Precipitation coupled with tiling chip).
ChAP-chip data for AbrB binding on the B. subtilis genome were taken from our previous report.
Thus, the ChAP-chip assay should be effective for proteins that are both stably and dynamically associated with genome DNA.
Our ChAP-chip analysis clearly shows that Spo0J forms a stable complex at eight regions, consistent with previous results.
In this study, we developed a ChAP-chip method, based on our original protocol for the purification of protein complexes.
Thus, it appears that our ChAP-chip method is sufficiently sensitive to detect the in vivo interaction sites of DNA-binding proteins.
This method combines in situ DNase I digestion of bacterial genomic DNA with a modified ChIP-chip method (ChAP-chip, Chromatin Affinity Precipitation-chip) we previously developed.
To improve versatility, this procedure was adapted for the purification of protein DNA complexes, denoted ChAP-chip (Chromatin Affinity Precipitation coupled with high density tiling chip).
H-NS and Hha binding profiles were determined using a slight modification of the previously described ChIP-chip and ChAP-chip methods.
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