GSE194320
RNA-Seq analysis of wild type Pseudomonas aeruginosa adhered to a surface for 5, 10, 15, 30, 45, or 60min
Purpose: Use RNA-seq to investigate the kinetics of bacterial response during the first hour of surface attachment Methods: Logarithmic phase bacterial culture in LB with optical density 600 (OD600) of 0.5 was inoculated in an Ibidi µ-Slide. At the indicated time from 5 - 60 min post-attachment, the channel was rinsed twice in PBS to remove non-adherent cells and 200µL of Trizol was added to the channel. Trizol was collected and stored at -80°C for RNA isolation. HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads from the 15 total samples, with a mean quality score of 37.4. Reads were aligned to the reference PAO1 genome using Rockhopper. Results:In total, 453 genes were differentially regulated between 5 min post-attachment, and at least one of the later time points. Expression of most of the regulated genes was elevated (390 genes) rather than reduced (63 genes) upon surface attachment Conclusion: This rapid response indicates that biofilm phenotypes may occur more rapidily than previously proposed, and that the phenotype may be triggered by surface contact Overall design: RNA-Seq analysis of wild type Pseudomonas aeruginosa adhered to a surface for 5, 10, 15, 30, 45, or 60min. Each time point was analyzed in triplicate