RNAseq

Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files (.fastq) were processed in the following manner: (i) All reads from the same individual were merged into one fastq file. (ii) Reads were mapped to the Atlantic salmon genome (GenBank Accession number: GCA_0002333375.4) using STAR (v 2.6.0c) 50. (iii) Read alignments, recorded in BAM format were subsequently used to count uniquely mapped reads per gene using featurecounts (v1.4.4) 51, with the RefSeq gene_ids. Raw illumina reads as well as gene counts are publicly available through ArrayExpress 52 accession E-MTAB-7220.