Profiling Mtb expression during hypoxia and reaeration by RNA-seq

We hypothesized that transcription factor activities found to be predictive of overall Mycobacterium tuberculosis (Mtb) fitness in a pooled culture of transcription factor induction strains could also be used to predict growth phenotypes under other growth conditions using interpretable machine learning models. To test, we measured Mtb transcriptional responses grown under hypoxic and reaeration stress without recombinant transcription factor perturbation as input data for our modeling. Overall design: RNA-seq analysis was performed on samples taken from cultures subjected to a 12-day hypoxia and reaeration timecourse. Strains were cultured in oxygen-limited conditions for 7 days, followed by reaeration on days 7-12. Four biological replicates were maintained and sampled.