title: RNAseq of S. enterica monoculture; time = 6h
design: Cells were fixed in RNAlater (Invitrogen, CA, USA) according to manufacturer guidelines and pellets were frozen. RNA was extracted from thawed pellets using RNeasy spin column extraction with on-column DNase treatment, as per manufacturer instructions (Qiagen). The Illumina Stranded Total RNA Prep, Ligation with Ribo-ZeroTM Plus (Illumina, CA, USA) was used to conduct ribosomal RNA depletion and sequencing library synthesis with random hexamer primed reverse transcription. Samples were sequenced by paired-end sequencing on the Illumina NextSeq, which generated over 20 million reads per sample. PhiX control sequence was removed from reads. Reads were trimmed and filtered using trimmomatic.