Assessing the effects of transcription factor knockouts on growth in high-density fed-batch cultures

We used RNA-seq to investigate the effects of single transcription factor knockouts on growth of E. coli BW25113 in fed-batch cultures at multiple timepoints. Cells were grown in an ambr automated bioreactor and maintained at 30 degrees and pH 6.5 in Medium C. Growth of E. coli was performed with biological duplicates. Total RNA was extracted from fed-batch culture at specified time points for RNA-Seq library preparation. For batch cultures, total RNA was extracted at mid-log phase.