RNA-Seq
The ribo-depleted RNA was then enzymatically sheared to roughly 150bp using KAPAs HyperPrep RNA-seq kit (Roche # KK8540). KAPAs HyperPrep RNA-seq, kit along with Illumina-compatible adapters (IDT #00989130v2), was also used for the remaining library construction. Separate libraries were constructed and sequenced from RNA obtained from independent bacterial cultures. The adapter-ligated libraries were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with Kapas HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent Tapestation, and quantified by qPCR (KAPA KK4835) on Thermo Fisher Scientifics Quantstudio 5 before multiplex pooling and sequencing on a 2x75 flow cell on the NextSeq500 platform (Illumina) at the Arizona State University Genomics Core facility. RNA-seq reads for each sample were quality checked using FastQC v0.10.1 and aligned to Escherichia coli K-12 MC4100 genome assembly from NCBI Database (https://www.ncbi.nlm.nih.gov/assembly/GCF_000499485.1/) using STAR v2.5.1b.