Ribosomal RNA depletion was performed using the MICROB Express Bacterial mRNA Enrichment kit (Thermo Fisher Scientific, Massachusetts, USA) following the manufacturer’s protocol. The enriched mRNA was subjected to cDNA library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Massachusetts, USA). The library was then quantified using Qubit 2.0 fluorometer (Invitrogen, California, USA) and the size distribution was checked using TapeStation 2200 (Agilent Technologies,California, USA). All libraries were pooled equimolar and 15pM was loaded into the MiSeq cartridge. Sequencing was performed on the MiSeq system using a 2 × 75 bp run configuration.

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