title: RNA-Seq of E. coli  ELSA-MultiAux
design: Total RNA was extracted from cultured strains and its integrity confirmed using a Bioanalyzer (Agilent). Ribosomal RNA depletion was carried out using the Ribo-Zero rRNA Removal Kit for Bacteria (Illumina), except using ethanol precipitation instead of column-based purification to retain short RNAs, including sgRNAs. The integrity of rRNA depleted samples was again confirmed using a Bioanalyzer, followed by library preparation performed by the Penn State Genomics Core Facility. RNA-Seq was carried out using the TruSeq Stranded mRNA Kit (Illumina) and an Illumina NextSeq using 75 bp paired-end sequencing, obtaining 23-40 million raw reads per sample.