library_construction_protocol: Fly growth was performed as described previously for the modENCODE and modERN projects Kudron et al., 2018(PMID: 29284660). Transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22℃ and larvae, white pre-pupae(WPP) and adults were collected from these expansion vials. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22℃. For embryonic collections, 0-8 day old adult flies were moved to embryo cages capped with apple juice plates. After a 24 hour hours, apple juice plates were replaced at appropriate intervals, restricting the collected embryos to their desired developmental stages. For late embryonic stages, collection plates were removed and embryos were grown at room temperature until the desired stage was reached prior to chromatin collection.    Chromatin was collected and ChIP was performed using the goat anti-GFP as described previously Kudron et al., 2018 (PMID: 29284660).  However, later experiments were performed using Ab290 (Abcam) and denoted as such in Kudron et al., 2024; Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing. 