Mycobacterium tuberculosis Strain H37Rv

MTB H37Rv was used for all experiments with the single exception of one experiment performed in M. smegmatis (Supplementary Fig. 21). This MTB strain was fully sequenced by the Broad Institute (GI:397671778). For Chip-Seq, cells were cultured in Middle brook 7H9 with ADC (Difco), 0.05% Tween 80, and 50 µg ml⁻¹ hygromycin B at 37 °C with constant agitation and induced with 100 ng ml⁻¹ anhydrotetracycline (ATc) during mid-log-phase growth, and ChIP was performed using a protocol optimized for mycobacteria and related Actinomycetes. For the hypoxia and re-aeration time-course, bacilli were cultured in bacteriostatic oxygen-limited conditions (1% aerobic O₂ tension) for seven days, followed by re-aeration. Bacteria were cultured in Sauton’s medium without detergent or exogenous lipid source. Profiling samples were collected as described in the Supplementary Text. All data available at http://TBDB.org. Expression data also available at GEO (accession number GSE43466).