GSM8830685: ATRX-ChIP-seq_HUDEP-2_undiff_d0; Homo sapiens; ChIP-Seq
ATRX ChIP-seq was carried out on 50x10^6 cells following the optimised protocol described in Truch et al., 2018. Briefly, cells were double-fixed with firstly 2mM ethylene glycol bis succinimidyl succinate (EGS, Sigma, Cat No E3257) for 45 min and then 1% formaldehyde solution for 20 min at room temperature. The cross-linking was quenched with 125 mM glycine (Sigma-Aldrich, Cat No G7126). After cells lysis, the chromatin was fragmented using Covaris ME220 ultrasonicator followed by pre-clearing with Protein A/G Dynabeads (Invitrogen, Cat No 10001D, 10003D) before taking input controls and immunoprecipitation with 15 μg ATRX antibody (Abcam, Cat No ab97508). After sequential washes at 4°C, samples were eluted, de-crosslinked and proteinase K treated. DNA was precipitated using phenol/chloroform extraction and ethanol precipitation with GlycoBlue (15 mg/mL) (Thermo Scientific, Cat No AM9516) prior to dissolving in 20 μL of ultrapure water. Purified DNA was quantified using the Qubit dsDNA HS assay (Invitrogen, Cat No Q32854) and indexed using NEBNext Ultra II DNA library prep kit (NEB, Cat No E7645L). Libraries were quantified, and sequenced on an Illumina NextSeq machine with paired-end reads.