RNA-seq of E coli: pNOX cells
Overnight cultures grown in MOPS rich media were inoculated 1:500 into fresh media and grown to OD600  0.1. 600 L cells were then mixed with 1200 L RNAprotect Bacteria Reagent (Qiagen; Germantown, MD) to inactivate RNase activity. Total RNA was extracted using RNeasy Micro Kits (Qiagen). RNA concentrations and RNA integrity were measured on an Agilent 4200 TapeStation. Ribosomal RNA was depleted using the Ribo-Zero Plus rRNA Depletion Kit (Illumina; San Diego, CA). cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs; Ipswich, MA). RNA sequencing was performed on an Illumina NovaSeq6000 system with 100x coverage.