RNA-Seq of E. coli: RadH_1
RNA was extracted using either the RNeasy PowerFecal Pro Kit (Qiagen, Venlo, Netherlands) or RNeasy Mini Kit (Qiagen). The NEBNext rRNA Depletion Kit (Bacteria) (New England BioLabs, Ipswich, MA, USA) was used for ribosomal RNA depletion according to the manufacturers instructions. Libraries for Illumina sequencing were made with the TruSeq stranded mRNA library prep (Illumina) following the manufacturers protocol. RNA sequencing was performed on the NovaSeq 6000 platform (Illumina) using paired-end 150 bp sequencing. Image analysis was performed using the NovaSeq6000 control software version 1.3.1 and the output base calling data was de-multiplexed with bcl2fastq version v2.20.0.422, generating fastQC files.