RNA-seq of E. coli: WT MG1655-EcM2.1 strain collected at the stat phase grown in M9 (24 hours of growth)
Samples were grown in LB medium or M9, each started from a single and different colony. RNA was extracted at early log (OD600 of 0.1-0.2), mid-log (OD600 of 0.7-1), or stationary phase (24 hours of growth), as described above. Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit (Bacteria) (New England Biolabs, #E7850). RNA-seq Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7760). DNA-seq libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, #E7805L). Finally, RNA-seq libraries were sequenced on the NovaSeq X platform (Illumina).