RNA-seq of E. coli, S. enterica, and A. baumannii: pool of solo cultures at 0 h
Ribosomal RNA was depleted with the RiboMinus Transcriptome Isolation Kit (Invitrogen). DNase treatment was done for each sample using the TURBO DNA-free kit (Ambion), and cDNA template was synthesized by random priming using the Verso cDNA kit (Thermo Scientific). Samples were prepared for Illumina sequencing with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturers instructions. Samples were sequenced by paired-end sequencing on the Illumina MiSeq using the MiSeq Reagent Kit V3 2x75 cycle kit. PhiX control sequence was removed from reads.