Analysis of transcriptome changes in Neisseria gonorrhoeae exposed to sublethal levels of hydrogen-peroxide

We report 293 Neisseria gonorrhoeae genes that show differential transcript abundance in response to 15 mM hydrogen peroxide treatment by RNA-Seq. We analyze the major physiological functional groups of genes affected by hydrogen peroxide exposure. In addition, we analyze which genes in our hydrogen peroxide-responsive set of genes belong to major known transcriptional regulatory circuits like iron homeostasis, anaerobiosis and others. We annotate which of the 293 hydrogen peroxide-responsive genes belong to operons. We annotate global transcriptional start sites and identify transcriptional start sites that are only present in hydrogen peroxide-treated bacteria. We validate the RNA-Seq data for a subset of representative genes by RT-qPCR and whether transcript abundance in this same subset of genes differs upon treatement with other reactive oxygen species encountered during infection, like organic peroxide, super oxide anion, and bleach. Examination of transcriptional changes in sublethal 15 mM hydrogen peroxide-treated Neisseria gonorrhoeae in liquid culture compared to untreated controls Please note that the +TEX data was only used for visualization of peaks to determine transcription start sites (see the .wig files) and was not used in any way to quantify overall transcript abundances. Thus, the differential expression component of our analysis relied only on noTex samples and these are the only samples that were quantified (TPM) for.