As described previously, transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22°C. Larvae, white pre-pupae(WPP) and adults were collected from these expansion bottles. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22°C. For embryonic collections, 0-8 day old adult flies were transferred to embryo cages capped with apple juice plates. After a 24 hour preincubation, 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 maintained at room temperature prior to chromatin collection.
Chromatin was collected and immunoprecipitated (IP) using the goat anti-GFP described previously (Zhong et al. 2010 (link); Niu et al. 2011 (link); Kasper et al. 2014 (link); Kudron et al. 2018 (link)). However, due to its limited supply, later experiments used anti GFP Ab290 (Abcam) (Suppl. File 1). In total, ChIP was successfully performed for 677 (604 different TFs) experiments with TFs and another 63 experiments (56 different genes) for nonTFs. Of the 12 tagged TF strains without ChIP, six failed to yield data and for another six, ChIP was not attempted.