Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with streptavidin beads. The chromatin extracts containing DNA fragments with an average size of 500 bp were affinity purified using streptavidin beads. Purified DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.