GSM8150862: HEPA1-6, input rep 1; Mus musculus; OTHER
genomic extraction was performed following step by step: High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing, Sanz and Chedin, Nature protocol, 2018 Prior to library preparation DNA was sonicated in Covaris microtubes (Fisher, 520045) to a peak fragment size of 300 bp, performed on a Covaris machine S220 using the following parameters: Intensity: 4, C/B: 200. DF: 10%, Time: 30 seconds. NEBNext® End Repair Module (NEB, E6050S) was used to repair the sonicated DNA and successively 3' A-tails were added by Klenow Fragment (3'→5' exo-) (NEB, M0212S) and dATPs (NEB, N0440S). Next, adapters were ligated to the repaired DNA using the 1S Plus Set A Indexing Kit (Swift Biosciences), and DNA was then amplified by PCR (PE PCR Primer 1.0: 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3'; PCR Primer 2.0: 5' CAAGCAGAAGACGGCATACGA 3). For input libraries, 4 PCR cycles were used, while for IP libraries, 10 PCR cycles were needed. Following PCR amplification, DNA fragments between 200 and 600 bp were size selected using AMPure XP beads (Beckman Coulter, A63880). Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA) then pooled in equimolar ratios and sequenced on a HiSeq 4000 (Illumina, San Diego, CA, USA) at the Stanford Genome Sequencing Service Center, using 2x75bp sequencing