Total RNA was extracted from liver and skeletal muscle tissues of each individual fish using the PureLink Pro 96 RNA Purification Kit (Invitrogen), according to the manufacturer’s instruction. RNA was treated with PureLink On-Column DNase Digestion (Invitrogen) to remove any contaminating DNA. Samples were shipped to The Norwegian High-Throughput Sequencing Centre, where the mRNA library preparation and sequencing of transcripts were performed using standard protocols (www.illumina.com ). Samples were sequenced on an Illumina HiSeq platform as paired-end 151 bp reads. After final quality control, results from 48 liver- and 59 skeletal muscle samples remained for analyses.
Processing of reads, alignment and annotation was performed according to Moghadam et al.42 (link). Expression data were normalized via the median of the geometric means of fragment counts across all sample43 (link). Cufflinks and Cuffdiff were used to estimate the expression abundances of the assembled genes and transcripts44 (link).
Processing of reads, alignment and annotation was performed according to Moghadam et al.42 (link). Expression data were normalized via the median of the geometric means of fragment counts across all sample43 (link). Cufflinks and Cuffdiff were used to estimate the expression abundances of the assembled genes and transcripts44 (link).
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