RNA-Seq of Salmo salar
Total RNA was extracted from the mid- and hind intestine (n=3 or 4 per diet, a total of 23 samples). mRNA extraction was done using a RNeasy Plus Universal Mini kit (Qiagen, Hilden, Germany) according to protocol. RNA concentrations were measured using a Nanodrop 8000 (Thermo Scientific, Wilmington, USA), and RNA quality was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA). All 23 samples passed the quality check with an RNA Integrity number (RIN) higher than 7. cDNA libraries were prepared using TruSeq Stranded mRNA Samples prep HS protocol (Illumina, California, USA) according to instructions, with selection for 500 bp fragments. cDNA library was sent to Genomics Core Facility at the Norwegian University of Science and Technology (NTNU) for sequencing. Libraries were quantified by qPCR using the KAPA SYBR FAST library quantification kit for Illumina Genome Analyzer (KAPA Biosystems, Woburn, MA, USA). A 2.5 nM solution of the sequencing library pool was subjected to cluster generation on a HiSeq4000 flowcells by the cBot instrument (Illumina, Inc., San Diego, CA, USA). Double-end sequencing was performed for 2X75 cycles on a HiSeq4000 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions, producing 76bp double end reads. Base Base-calling was done on the HiSeq4000 instrument by RTA 2.7.7. FASTQ files were generated using bcl2fastq2 Conversion Software V2.20.0422 (Illumina, Inc. San Diego, CA, USA).