Marinade - Salmonella
200 ng of bacterial RNA in nuclease free water was reverse transcribed to cDNA according to the Oxford Nanopore cDNA-PCR sequencing kit protocol. The length and quantity of the cDNA obtained was assessed. The cDNA library was prepared according to a modified version of the Cut&Run library preparation protocol, using the NEBNext Ultra II DNA Library Prep Reaction Kit  (Liu, 2021). NEB adaptors were attached to the cDNA after an End prep PCR step. Amplicons were selected for according to size using AMPure XP beads and indexed according to an NEBNext Ultra II Q5 Index protocol and, after a second AMPure XP size-selection steps, final libraries were analysed. This denatured library was prepared according to Illumina MiSeq kit instructions, utilising a PhiX library control (1%). Barcoded cDNA libraries pooled concentrations of 4 nM and 15 pM, were denatured and loaded into a 150-cycles V3 flow-cell and sequenced with Illumina MiSeq.