Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 14 times in ice water bath followed by 1 minute pause at the highest setting. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 m filter units (cat. UFC30HV0S) at 13,000 rpm, 4C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/. Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Qiagen kit. For a detailed protocol see http://www.modencode.org/. Solexa_Library_Prep_vKI3 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel.