Transcriptional Response of S. pneumoniae to AI-2

S. pneumoniae strains were grown in C+Y without added sugars to an OD₆₀₀ of 0.15 and then treated with or without 10 μM AI-2 for 30 min. RNA extraction was performed with a Qiagen RNase minikit according the manufacturer’s protocol. Each sample was derived from three independent cultures (biological replicates) and pooled prior to transcriptome sequencing (RNA-seq) analysis. Total RNA was submitted to the Australian Genome Research Facility (Melbourne, Australia) for sequencing. Briefly, the Epicentre Bacterial Ribozero kit (Illumina) was used to reduce the rRNA content, and then the Ultra Directional RNA kit (New England Biolabs) was used to generate bar-coded libraries. Prepared libraries were then sequenced with the Illumina HiSeq 2500. Trimmed RNA-seq fastq files were then mapped to the D39 reference genome with BOWTIE2 version 2.2.3 (43 (link)). Counts for each gene were obtained with the aid of BEDTools (44 (link)), and differential gene expression was examined with DESeq (45 (link)).