RNA-SEQ of Salmo trutta fario liver
From samples of individuals with comparably high immune response (according to the NMDS) strand-specific rRNA-depleted RNA-seq libraries were prepared using the Ovation Universal RNA-Seq System (NuGen Technologies, Leek, Netherlands) following the manufacturers specifications in combination with 324 InDA-C primers designed by NuGEN to target salmonid 18S and 28S rRNA transcripts for depletion. Sequencing libraries were quantied, pooled in equimolar concentration and sequenced on the next-generation sequencing platform Illumina HiSeq 2500 (Illumina, San Diego, CA, USA) producing 2  100-nucleotided single-end reads. For quality assessment and trimming, the raw reads were screened with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).