Identification of transcription start sites in Campylobacter fetus subspecies fetus 82-40 and venerealis 84-112 using dRNA-seq

C. fetus subsp. fetus 82-40 and C. fetus subsp. venerealis 84-112 RNA were grown on CBA plates for 24h. To construct differential cDNA library pairs, was RNA was isolated from the bacterial cells and aliquots of extracted RNA from each strain was treated with Terminator-5'-phosphate-dependent exonuclease (TEX; Epicentre) to deplete processed RNAs (denoted TEX+) in addition to untreated RNA (denoted TEX-). Construction of cDNA libraries was performed by vertis Biotechnology AG (Munich, Germany). Libraries were sequenced using cluster amplification with the TruSeq PE Cluster Kit v.5 on a cluster station. Each library was sequenced on a single HiSeq 2000 lane using TruSeq SBS 36 Cycle Kits v.5 (Illumina, San Diego, CA) and a 91 bp single-end protocol. Sequencing image files were processed with the Sequencing Control Software (SCS) Real Time Analysis (RTA) v2.6 and CASAVA v.1.7 (Illumina). Reads were mapped to the reference genomes using the CLC Genomics workbench (CLC Bio) with default settings. Transcription start sites were identified using a the strand specific coverage information from the mapping.