Nextera tagment dna enzyme

BJ cells (passage 19) were harvested at 70% confluence using Accutase and washed twice with ice-cold PBS. Aliquots (8,000 cells) were pelleted for 5 min at 500g in 1.5 mL tubes at 4 °C, and resuspended in 50 μL of transposition mix containing 2.5 μL Nextera Tagment DNA Enzyme (Illumina), 1× Nextera Tagment DNA Buffer (Illumina), and 0.01% digitonin (Promega), using a modified ATAC-seq protocol^{36 (link)}. Transposition reactions were performed at 37 °C with 300 r.p.m. mixing for 30 min. Libraries were purified with a QIAQUICK PCR cleanup kit, eluting with 20 μL, and amplified with NEBNext 2 × PCR Master Mix (New England Biolabs) using barcoded PCR primers (Supplementary Table 1) for variable numbers of cycles (~10) determined by using qPCR on an aliquot to avoid saturation. Amplified libraries were purified with a QIAQUICK PCR clean up kit and size-selected with a 2.5% agarose gel and MinElute Gel Extraction Kit before high-throughput sequencing on an Illumina HiSeq 2500 (50 bp paired end reads; ELIM Biopharm). Eight technical replicates were performed and data was pooled for peak calling and nucleosome calling (see below).