Illumina HiSeq 2500 paired end sequencing
The pre-cultures of triplicates of A. wodanis 06/09/139, ∆ainS and ∆litR were grown at 6°C and 12°C at 220 rpm and harvested at low cell density (LCD) OD600 =2.0 and high cell density (HCD) OD600 =6.0. Cultures were harvested and mixed and incubated with RNAprotect Bacteria reagent (Qiagen, Germany). After centrifuging, the total RNA from the cell pellets were isolated using the MasterpureTM complete DNA/RNA purification kit (Epicentre, Cambio Ltd., Cambridge). The RNA concentration was measured in NanoDropTM 2000c spectrophotometer (Thermoscientific, DE, USA). Ribosomal RNA (rRNA) was depleted from the total RNA using Ribo-zero rRNA removal kit for bacteria (Illumina, San Diego, CA, USA). The RNA quality before and after rRNA depletion were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The mRNA libraries were prepared using the TrueSeq stranded mRNA library kit (Illumina) and sequenced on Nextseq 500 (Illumina, USA) using 150 cycles mid-output kit and run as a 75bp paired end reads at NorSeq (The National Consortium for Sequencing and Personalized Medicine). The image analysis and base calling were performed using Illumina's RTA software version 2.4.6.