Exactly ten million cells were pelleted and fixed with formaldehyde. Nuclei were harvested upon cell lysis, at which time drosophila S2 cell nuclei were spiked into cells in lysis buffer at one S2 cell nucleus per five experimental cells. Probe sonication (micro tip, 30 amplitude, 30” on, 8 cycles) was optimized for Nalm6 cells. Special attention was paid to equal and consistent volume transfers. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were 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.