Genome-wide strand-specific R-loops mapping in E. coli DY330 using DRIP-Seq

Distribution of R-loops on genomic sites was studied for exponentially growing Escherichia coli in different conditions using strand-specific DRIP-Seq with S9.6 antibodies. Overall design: Total nucleic acids were extracted from E. coli DY330 culture growing in LB medium (exponenrial phase, OD600=0.6). Cultures were either untreated (i), or treated with 100 mkg/ml rifampicin for 20 min (ii, Rif), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min (iii, CTD), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min and then 100 mkg/ml rifampicin was added for 20 min (iv, CTD/Rif). R-loops were enriched with S9.6 antibodies and prepared for sequencing using Accel-NGS 1S kit. Sample treated with RNAse HI before enrichment with the antibodies served as a control. For each condition 3 biological replicates were processed and sequenced.