Rainbow trout infected with P. salmonis LF89 (infected)
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, TX, USA) following the manufacturers instructions. RNA was quantified through spectrophotometry using NanoDrop technology with the Epoch Multi-Volume Spectrophotometer System (BioTek, VT, USA).  Total RNA isolated from skeletal muscle was treated with DNase I to remove genomic DNA. RNA concentration was measured by Qubit 2.0 Fluorometer (Life Technology, Carlsbad, CA, USA) and RNA integrity was determined using Fragment Analyzer Automated CE System (Analytical Advanced Technologies, Ames, IA, USA). Equal quantity of total RNA from four fish was pooled by conditions, and the total RNA was used to prepare mRNA libraries. cDNA libraries were constructed using TruSeq RNA Sample Preparation kit v2 (Illumina, USA).  Libraries were sequenced (2 x 250bp) by MiSeq (Illumina) platform.