Comparison of enteroaggregative Escherichia coli strain 042 transcriptome with an aggR mutant using RNA-Seq.

An enteroaggregative Escherichia coli aggR mutant and the parental strain 042 were inoculated into DMEM high glucose to an OD600 of 0.05. The cells were grown to mid-log phase at 37°C. Cells were harvested by centrifugation and RNA was extracted using QIAGEN RNeasy kit. Ribosomal RNA was removed using the Ribo-Zero™ Magnetic Kit (epicenter®, Illumina). RNA depleted of rRNA was converted to cDNA using TrueSeq® Stranded mRNA LT Sample Prep Kit (Illumina). Pair-end reads, 75 bp in length, were generated from the cDNA library using MiSeq Desktop Sequencer (Illumina). Reads were used to determine the differential expression of genes in the aggR mutant compared to the wild-type strain.