RNA-seq of Escherichia coli: RSG_B012 - 2h arabinose
Total RNA was extracted from E. coli using the Nucleospin RNA Extraction Kit (Macherey-Nagel) according to manufacturers instructions. DNAse was depleted using an additional DNase treatment with Turbo DNase (Thermo Fisher). The DNAse was inactivated and RNA purified by a phenol-chloroform extraction (pH 4.5, Amresco) and ethanol precipitation. The RNA was then resuspended in DEPC-treated water. Ribosomal RNA depletion was done using Ribo-Zero magnetic beads according to manufacturer protocol (Illumina). cDNA library preparation was performed following standard protocols. Briefly, RNA was fragmented using the NEBnext mRNA first and second strand synthesis kits (NEB). One to three biological replicates were generated for each condition and on average ~10 million reads were generated per sample.