RNASeq files for fish health in N Johnstone River, Barratta Creek, Wenlock Catchment

These files illumina sequencing reads representing the hepatic transcriptome of wild caught barramundi from Barratta Creek (353-360), N. Johnstone River (402-406) or the Wenlock Catchments (WC1-5; WC55,56).\nLineage: Fish collections \nBarramundi were collected as described previously (Kroon et al., 2015a) with the approval of the CSIRO Sustainable Ecosystems animal ethics committee (permit #13-12). Briefly, barramundi were captured in 2011 or 2012 with exact dates provided in Table 1. Monofilament gill nets (50 mm stretched mesh) were used to capture fish. Fish were anaesthetised with clove oil, then sacrificed by gill slitting and cervical dislocation. Fish were measured (mm, total length, TL), weighed (g), then liver tissues were harvested and small samples preserved in RNA later© (Ambion). Samples were kept on ice until delivery to the laboratory then stored at -20°C until further processing.\nRNA extraction\nAn overview of the workflow used during the RNA-Seq experiment is provided in Figure 2, and was described previously in Hook et al, in revisions. RNA was extracted as described previously (Kroon et al., 2015a; Kroon et al., 2014). Briefly, approximately 20 mg of liver tissue was immersed in TRIzol© (Invitrogen) reagent, homogenized using MP Biomedical© bead beater and lysing matrix E tubes, then extracted following the TRIzol© protocol through the removal of the aqueous phase. Hereafter, RNA was purified using the Ambion Purelink. After extraction, the TURBO DNA free© (Ambion) kit was used to eliminate genomic DNA contamination. RNA purity was determined using a nanodrop spectrophotometer (260/280 ratio greater than 2.0) and integrity determined using an Agilent bioanalyzer© (RIN greater than 7.0). \nSequencing\nSequencing for this project was performed at the Australian Genome Research Facility. Briefly, cDNA synthesis and library preparation was carried out using a starting template concentration of 1 µg RNA. Illumina’s TruSeq stranded mRNA sample preparation was used and the manufacturer’s protocol was followed. The samples were run on an Illumina HiSeq 2000 with 100 base pair reads.