Cut&Run of danio rerio: 15-18s tailbud
CUT&RUN experiments were done in duplicates for HS:hoxa13b-FLAG-GFP, HS:rbpja-FLAG-GFP and histone mark H3K4me1 and H3K27ac, and triplicates for KI:hoxa13b-FLAG-GFP. DNA fragements cut by the pAG/Mnase were extracted and used for NGS library preparation. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit, NEB (Ipswich, USA) for transcription factors following the protocol of Liu (https://dx.doi.org/10.17504/protocols.io.wvgfe3w), with some modifications for histone marks due to larger Cut&Run fragment size (Meers et al., 2019). Modifications for histone mark samples include: 1) In step 2, PCR program for End Prep 20C for 30 min, 58C for 45 min and hold at 4C; 2) In step 8, 1.5 X AMPure XP beads size selection was applied after adaptor ligation; 3) In step 19, 0.65 X AMPure XP beads size selection was applied for the first round size selection to remove PCR products larger than 500 bp.