GSM5224911: E14_ADNPKO_RNA-Seq_Rep1; Mus musculus; RNA-Seq
CUT&RUN for CTCF, ADNP, and HA was performed on cells as previously described (Skene and Henikoff, eLife 2017). R-loop containing DNA was collected using MapR protocol as previously described (Yan et al., Cell Reports 2019). Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen). rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760). DNA 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.
GEO Accession
GSM5224911