RNA-Seq profiles of early responses to antibiotics in clinical isolates

These data represent timecourses of RNA-Seq transcriptional profiles of Klebsiella pneumoniae (Kp), Escherichia coli (Ec), or Acinetobacter baumanii (Acb) upon treatment with either meropenem (Mero; 2 mg/L), ciprofloxacin (Cip; 1 mg/L), or gentamicin (Gent; 4 mg/L). In brief, two susceptible (S_rep1, S_rep2) and two resistant (R_rep1, R_rep2) clinical isolates of each species were grown at 37C in Mueller-Hinton broth from a frozen stock to mid-logarithmic phase, back-diluted >10-fold, regrown to early logarithmic phase, then split into two parallel cultures, one of which was left untreated, the other exposed to antibiotic. At the time indicated in the filenames (0, 10, 30, 60, or 120 minutes), cells were pelleted and total RNA was harvested by Trizol/chloroform extraction, then subject to library construction by the RNA-tagSeq method and sequenced on an Illumina platform (either NextSeq or HiSeq 2000 in paired-end mode). Data are archived as aligned bam files, with reads aligned to the reference genome indicated in the filename, which was determined to be the RefSeq genome with the closest match on average across the four clinical isolates.