GSM8605720: Confined Treated Replicate 3; Homo sapiens; ATAC-seq
50,000 cells for two biological replicates, for each treated condition, was collected and treated with transposase Tn5 (Nextera Tn5 Transposase; Illumina Cat #FC-121-1030). DNA was purified using AMPure XP beads to remove large fragments (0.5 × beads; >1kb) and small fragments (1.5 × beads; < 100bp). Samples were then amplified using NEBNext high-Fidelity 2x PCR Master Mix (New England Labs #M0541) with primers containing a barcode to generate the libraries, as previously described. Each condition was amplified using a combination of the P7 forward primer and a P5 reverse primers containing multiplexing adaptors, and sequenced accordingly to allow for segregation of reads. The number of cycles of library amplification was calculated as previously described. DNA was purified using a MinElute PCR Purification Kit (Qiagen), and samples were sequenced using an Illumina NextSeq2000 at the CRG Genomics Core Facility.