title: RNAseq of Salmo trutta m. fario adult muscle tissue
design: The TruSeq RNA sample Prep Kit (Illumina, Madrid, Spain) was used to build cDNA libraries according to manufacturer instructions. Briefly, from each tissue, cDNA was synthetized from the RNA pools (Brain tissue pool 10.2 g and muscle tissue pool 11.4 g) and double strand DNA was generated by PCR amplification. Then, cDNA fragments were end repaired, A-tailed and indexed adapters were ligated. Brain and muscle tagged cDNA libraries were pooled and used for paired-end sequencing on Illumina HiSeq2500 (Stab Vida, Lisbon, Portugal).The FASTQ sequence reads were generated using the Illumina Casava pipeline version1.8.3. Initial quality assessment was based on data passing the Illumina Chastity filtering. Subsequently, reads containing adapters were removed. The quality of the FASTQ sequences was enhanced by trimming off low-quality bases using the Trim sequences option. The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.10.0.