Binding of the Capicua repressor in response to pulses of ERK signaling in the early Drosophila embryo

We have measured by ChIP-seq the binding of Capicua transcriptional repressor (Cic) in Drosophila melanogaster embryos at early nuclear cycle 14. We compared binding in response to ERK activation, utilizing optogenetics. Overall design: Capicua was endogenously tagged with super-folder GFP, and ChIP-seq was performed using a GFP antibody. We evaluated binding of Cic in response to pulses of ERK activation, controlled using an optogenetic construct known as OptoSOS. Cic binding was measured in WT embryos, and optogenetic embryos exposed to no light,1 minute of light, 5 minutes of light, or 30 minutes of light. Cic binding was also measured in embryos with constitutively active Torso receptor (TorD4021) as a control. OreR embryos ChIPped with the GFP antibody were used as a negative control, to understand what the GFP antibody non-specifically pulls down. All samples, except for the 1 minute light condition, were done with 3 biological replicates. The 1 minute light condition had 2 biological replicates. Lastly, 1% inputs for all samples were also sequenced