GSM2716940: ESS_FAIRE_1; Homo sapiens; FAIRE-seq
DNA was recovered from fixed tissue sonicated in 5% SDS followed by phenol-chloroform extraction DNA fragments underwent end repair with T4 DNA polymerase, Klenow DNA Polymerase , and T4 polynucleotide kinase. Following purification with Agencourt AmPure XP DNA-binding beads in polyethylene glycol (PEG) at a 1.9:1 bead: DNA volume ratio, adenine bases were added to the ends of each fragment with Klenow exonuclease. Pre-annealed Illumina adaptors were ligated overnight at 16°C with T4 DNA ligase. Unligated adaptors and adaptor dimers were removed with an AMPure XP bead purification (1.2:1 bead: DNA) performed twice. PCR following adaptor ligation was performed with Phusion High-Fidelity DNA Polymerase (ThermoScientific F-530L) using unique Illumina TruSeq DNA LT indexing primers for 12-14 amplification cycles. Following PCR, amplified DNA underwent a final AmPure XP bead purification at a 1.1:1 or 1:1 PEG to DNA volume ratio.