Grainy head ChIP-seq from Drosophila wing discs

100 lightly fixed imaginal wing discs were used for each sample. For Cut&Run [20 (link)], the protocol provided with the Cell Signaling Cut&Run Kit (CAT: 86652S) was used with the following minor modifications and specifications: (1) 200uL (instead of 1 mL) of 1x Wash Buffer was used to dounce homogenize the wing discs to ensure efficient pelleting, (2) the provided spike-in DNA was added at 1:100 dilution, and (3) for each sample, we used 3uL of a Grainy head antibody that targets an epitope on the C-terminus of Drosophila Grh [21 (link)]. To construct Cut&Run libraries, the NEB Ultra II Kit was used with the following modifications as described in [22 (link)], to adapt the manufacturers protocols for Cut&Run library preps of transcription factors. The fragment distribution of each sample was visualized with BioAnalyzer to confirm the presence of ~ 200-250 bp peaks representing TF-bound regions. Libraries were sequenced on Novaseq S4 300 cycle at the University of Michigan.