DvH-MO planktonic 1.5 mM indole rep a2
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit with On-Column DNase I treatment and quantified using Qubit 2.0 Fluorometer. RNA integrity was checked with 2100 Bioanalyzer. Whole transcriptome RNA enrichment was performed using Ribozero rRNA Removal Kit. RNA sequencing library preparation was prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturers recommendations  Sequencing libraries were validated using a DNA Chip on the Agilent 2100 Bioanalyzer  and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR. The sequencing libraries were multiplexed and clustered on six lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 2500 instrument according to manufacturers instructions.  The samples were sequenced using a 2x100 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq 2500 instrument.