RNA extractions, cDNA synthesis, and quantitative PCR

Strains were grown in LB medium and collected at 0.3–0.6 OD₆₀₀ for RNA extraction. Pellets were lysed and prepared following the standard protocol in Rneasy kit (Qiagen, Cat#). Following RNA extraction, samples were removed of any contaminating genomic DNA using the Dnase I standard protocol (Invitrogen, 18068015). Following Dnase treatment, RNA extracts were synthesized into cDNA using reverse transcriptase SuperScript^™ IV First-Strand Synthesis System (Invitrogen, Cat#). Finally, all cDNA samples were run on PCR to confirm no genomic DNA contamination before quantitative PCR. All cDNA samples (3 biological replicates) were run in SsoAdvanced^™ Universal SYBR^® Green Supermix (Bio-Rad, 1725271) in 3 technical replicates for 40 cycles. All primers are listed on Supplementary Table 2. ΔΔCq values were calculated using housekeeping gene rpoB as a control.