GSM7594350: H1563-DKO-r3; Homo sapiens; ATAC-seq
Profiling of chromatin was performed by ATAC-Seq as described by Buenrostro, et al. Briefly, approximately 50,000 viably frozen cells were washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 10-13 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced using the Reagent Kit (200 Cycles) (Illumina).  An average of 76 million paired reads were generated per sample. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688. Epub 2013 Oct 6.