title: RNA-Seq of untreated C. difficile R20291
design: rRNA depletion was performed using Ribozero, library preparation performed using NEBNext Ultra RNA Library Prep Kit for Illumina. Synthesized cDNA fragments were end repaired and adenylated at 3ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were quantified with Qubit 2.0 Fluorometer (Invitrogen) as well as by quantitative PCR (Applied Biosystems). The sequencing libraries were multiplexed, clustered on one lane of a flowcell and loaded on the Illumina HiSeq with paired End (PE) configuration.