RNA-Seq of Planktonic P. aeruginosa in flow

To determine whether flow alters the gene expression of planktonic P. aeruginosa, we designed a long microfluidic channel that enabled us to expose bacteria to flow for significant lengths of time and then be fixed as they exit the channel. The experiments mimic the kinds of shear flows characteristic of a wide variety of confined flow configurations. Using this microfluidic system, we performed bulk RNA-Seq analysis of planktonic bacteria that flowed for 55 min at a shear rate of 20 per second, and compared gene expression of this population with a control population of planktonic bacteria under similar conditions with no flow. We compared gene expression of planktonic bacterial cells that were subject to shear flow versus a control population of cells that were not subject to flow. Three biological replicates were used for each condition.