Following growth and treatment, 10mL aliquots of cells were pelleted and resuspended in 1mL TriReagent (Molecular Research Center), then lysed with 0.1mm silica beads in a bead beater (MP Bio). RNA was extracted by adding 200 uL chloroform, mixing, and centrifuging. The aqueous layer was extracted and added to one volume of 70% ethanol. RNA purification was completeted using the RNeasy minikit (Qiagen). First, the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 1ug of total RNA was used for ribosome RNA depletion with the Invitrogen™ RiboMinus™ Transcriptome Isolation Kit, bacteria.  After rRNA depletion, the libraries were prepared following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads.
GEO Accession
GSM4458970