Pseudomonas aeruginosa rRNA depletion RNA-seq analysis

Depletion of ribosomal (r)RNA is essential in the preparation of bacterial RNA-seq libraries. While a number of bacterial rRNA depletion procedures, demonstrating variable efficiency, have become available, comparative evaluation of these methods has remained limited. This project was aimed at evaluating the efficiency of three kits (Illumina Ribo-Zero rRNA Removal Kit [Bacteria], Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit, and Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria) in depleting rRNA from samples derived from the opportunistic human pathogen Pseudomonas aeruginosa grown as biofilms. This is the first such evaluation performed for P. aeruginosa or for bacterial biofilm samples, a comparison made more important by the findings of biofilms have higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis.