title: Brassica napus westar infected with Leptosphaeria maculans at 7 dpi
design: For RNA-seq analysis, B. napus cotyledons were infected with Lmb, Lbc or water (control mock inocula), and at 7 and 14 days post inoculation (dpi) tissue around the inoculation site was harvested using a cork borer (0.5 cm diameter) and then placed into liquid nitrogen before freeze drying and subsequent grinding under liquid nitrogen. RNA was extracted using Trizol reagent from infected tissue and from mycelia of Lmb and Lbc from 7-day still cultures grown in oilseed rape medium. RNA was then DNAase-treated.     The two biological replicates of each sample with the highest RNA integrity number (RIN) values (> 6) were sequenced with Illumina TruSeq version 3 chemistry on an Illumina HiSeq2000 sequencer at the Australian Genome Research Facility. In vitro derived RNA was sequenced with 100 bp paired-end reads in order to aid gene annotation, and in planta derived RNA was sequenced with 100 bp single-end reads. A total of 15.5 Gbp sequence was generated from the in vitro libraries of the two fungi (7.75 Gbp per sample), and 72 Gbp sequence was generated from 12 in planta libraries (6 Gbp per sample). Reads were trimmed to a minimum phred score of 20 using Nesoni sequence software and remaining adaptor sequences were removed. Trimmed reads were aligned to a reference genome sequence with Tophat v1.4.1 splice-junction mapper. Reference genomes were Lmb isolate v23.1.3, Lbc isolate J154 (Rohan Lowe and Angela Van de Wouw, unpublished), and a Brassica exon array curated unigene set representing 135,201 gene models from B. napus, B. rapa and B. oleracea. Aligned reads were quantified using Cufflinks v1.0.3 transcript assembly and quantification software and denoted as average expression levels (FPKM - fragments per kilobase of exon per million mapped reads).