GSM9513314: mESC_ASVdTAG13_ADNP; Mus musculus; ChIP-Seq
ChIP for ADNP and CTCF was performed on cells as previously described (Trizzino et al., Cell Rep. 2018). Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen). HiC was performed using the Arima Genomics Hi-C+ for High Coverage kit. rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760). ChIP samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute. HiC samples were prepared using the NEBNext Ultra II DNA Library Prep Kit with modifications according to the Arima Genomics Hi-C kit.