RNA-seq expression analysis of E.coli in rich-M9 medium for HGT study

We have estimated the fitness effects of horizontally transferred Salmonella genes to E.coli. To better understand the role of protein-protein interactions, we want to identify the expression levels of known interaction partners of the transferred genes. Gene expression of E.coli carrying the plasmid with an mCherry gene under the control of the pLtet0-1 promoter, after 1 hour of induction with 5ng/mL Anhydrotetracycline, grown in rich M9 medium until OD 600: 0.12, in deep well plates, each well containing 1mL. Total RNA is isolated from the total volume of 16mL.