Transcriptome response of Atlantic salmon (Salmo salar) to a new piscine orthomyxovirus

This collection includes the paired-end Ilumina raw sequences from a transcriptomic experiment. Samples were obtained by challenging Atlantic salmon post-smolts with Pilchard orthomyxovirus (POMV), a new aquatic virus of concern to the salmon industry in Tasmania, Australia. The experiment includes triplicate samples of two tissues (liver and head kidney) from four groups: (1) a pre-challenge negative control, (2) a group of POMV-suspect moribund fish , (3) a group of POMV-positive moribund fish, and (4) a group of survivors. POMV-positive moribund fish were those that tested positive to the real-time PCR, with a cycle threshold (CT) value smaller than 38 in both tissues (liver and head kidney). POMV-suspect moribund fish were those with either no CT or a CT larger or equal to 38. Survivors were fish exposed to POMV, which were still alive at the end of trial (20 days after the start of the trial) and showed no clinical signs of disease.The aim of this study was to examine the molecular response of Atlantic salmon post-smolts to the infection with POMV in vivo following an injection-cohabitation challenge experiment in seawater.