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. Overall design: 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.