Embryos (1-3 hours post egg laying) were collected with embryo wash (0.03% Triton-X100 and 140mM NaCl) and dechorionated in 100% bleach for 2 minutes. For each experiment, six aliquots each of 100ul of embryos were transferred to Eppendorf tubes containing 340ul of buffer A1 (15mM HEPES pH 7.5, 15mM NaCl, 60mM KCl, 4mM MgCl2, 0.5% Triton X-100, 0.5mM DDT, and complete EDTA-free protease inhibitor cocktail (Roche)). To each tube, 37% formaldehyde was added to a final concentration of 1.8%. Embryos were then homogenized with an Eppendorf micropestle and fixed on ice for 15’. Cross-linking was stopped by adding glycine to a final concentration of 0.125M. Homogenates were then centrifuged for 3’ at 3000 rpm in a microcentrifuge at 4°C. Supernatant was discarded and 340 ul buffer A1 was added to each tube. Pellets were suspended by vortexing and centrifuged two more times (three washes with buffer A1 in total), followed by two washes in 340ul buffer A2 (15mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton-X100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche)). Pellets were then harvested by centrifuging at 14,000 rpm, snap-frozen in liquid nitrogen, and stored in -80°C for long-term storage. For each ChIP experiment, pellets were combined to yield 60 mg total, and sonicated in 200 ul buffer A2. Sonication was performed 4 times 30’’ on and 30’’ off with a Sonic Dismembrator Model 550 (Fisher Scientific) equipped with a microtip at power setting 3. Affymetrix/USB ChIP Assay Kits were used for immunoprecipitation. Libraries were made with NEXTflex™ ChIP-Seq Kit (BIOO Scientific, #5143-01) and barcoded with NEXTflex™ ChIP-seq Barcodes (BIOO Scientific, #514120).