Choose your protocol:For Henikoff lab protocol, please see their Nature Protocol paper.Why?The difference between NEB stem loop adaptors and illumina adaptors are their lengths. When ligated to both ends of DNA, they add 64bp and 124bp respectively. This makes huge difference when you do beads based cleaning up.What is this protocol?This protocol is based on library preparation manual of “NEBNext® Ultra™ II DNA Library Prep Kit for Illumina”, NEB E7645, and is specifically modified to make libraries from small DNA fragments (25-70bp). We have successfully applied this protocol to make libraries for CUT&RUN experiments and showed that it greatly increased the preservation of small fragments (Liu, Cell 2018. Fig. S2B [pdf])