CIRCLE-seq
Fragmented genomic DNA was end-repaired, A-tailed and the CIRCLE-seq adapter oSQT1288 was ligated to cap fragments. Uncapped fragments were removed by exonuclease treatment. DNA fragements were then circularised by  USER/T4 treatment followed by T4 ligation. Non-circularised DNA was removed by Plasmid-Safe ATP-Dependent DNase treatment. Samples were then treated either with Gyrase or not, before treatment with Cas9, or no Cas9 control. After Cas9 treatment library was A-tailed, NEBNext adapter was ligated (#E7601A), USER treated and PCR amplified with NEBNext i5 and i7 primers.