H3K9me3 Cut&Run-seq (with MNAse pretreatment) on untreated HeLa cells
Briefly, nuclei were embedded in LMP agarose and lysed with 1% Triton X-100 in PBS/EDTA. After lysis, the chromatin was either treated with Micrococcal Nuclease or left untreated. Sample was labeled with an antibody specified, washed and pAG/MNase was added. After washing antibody bound pAG/MNAse was activated with CaCl2 and the sample was incubated for 30 mins of ice. The eluted DNA was purified, then quantified with a Qubit fluorometer. ChIP-seq libraries were prepared by Illumina according to manufacturers instructions.