Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 % sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract was spiked in with 0.1-0.2 mg of C. Briggsae AF16 extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.