Transcriptional profiling of Mycobacterium tuberculosis exposed to proton pump inhibitor treatment in broth culture.

We hypothesized that an improved Mtb TRN could be inferred using a large, diverse compendium of RNA-seq data and therefore sought to supplement the existing repository of Mtb expression data available on SRA with additional conditions that could inform on Mtb's underlying regulatory programs. We profiled Mtb transcriptional response to a range of different proton bump inhibitor exposures in 7H9 broth culture by RNA-seq. Compound abbreviations: (PAN = pantoprazole, RAB = rabeprazole, VER = verapamil, LAN = lansoprazole, OMP = omeprazole). We went on to infer Mtb's TRN using a collection of inference methods in combination with this compendium, and employed it to build an interpretable machine learning model of Mtb fitness under stress. RNA-seq analysis was performed on samples taken from Mtb cultures subjected to various stresses.