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.

本数据集涵盖肺炎克雷伯菌（Klebsiella pneumoniae, Kp）、大肠杆菌（Escherichia coli, Ec）及鲍曼不动杆菌（Acinetobacter baumanii, Acb）经美罗培南（meropenem, Mero; 2 mg/L）、环丙沙星（ciprofloxacin, Cip; 1 mg/L）或庆大霉素（gentamicin, Gent; 4 mg/L）处理后的RNA测序（RNA-Seq）转录组时间进程数据。
简要而言，针对每一种受试菌种，我们选取2株敏感临床分离株（S_rep1、S_rep2）与2株耐药临床分离株（R_rep1、R_rep2）：从冷冻菌株储备液复苏后，于37℃的穆勒-欣顿肉汤（Mueller-Hinton broth）中培养至对数中期，按大于10倍的比例进行二次稀释后继续培养至对数早期，随后将菌液分为两组平行培养——一组为未处理对照组，另一组加入抗生素进行胁迫处理。
在文件名标注的时间点（0、10、30、60或120分钟）收集菌体，通过Trizol-氯仿提取法获取总RNA；随后采用RNA-tagSeq法构建测序文库，并在Illumina测序平台（采用NextSeq或HiSeq 2000双端测序模式）上完成高通量测序。
所有数据以比对后的BAM文件形式存档，测序读段比对至文件名中指定的参考基因组；该参考基因组为经比对确定的、在四株临床分离株中平均匹配度最高的RefSeq参考基因组。