RNA sequencing based analysis of the bacterial transcriptome. Escherichia coli BW38028

To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. Overall design: E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.

为探究大肠杆菌K-12（E. coli K-12）的转录组结构，我们采用两种RNA测序（RNA-Seq）技术，以单核苷酸分辨率分析链特异性转录。我们通过一套标准化分析框架处理数据，以此注释全基因组范围内定义转录单元的启动子与终止子。研究发现复杂操纵子内存在显著的差异基因表达证据，我们基于操纵子结构对其进行了分类。
整体实验设计：将大肠杆菌K-12菌株MG1655的亚株BW38028及其同基因背景的rpoS突变株，接种于限碳、限氮或限磷的葡萄糖最小培养基中，分别采集对数生长期与稳定生长期的样本，对其总转录组进行测序。