RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout
RNA was extracted from the muscle by using TriZol (Invitrogen, Carslsbad, CA, USA), followed by quantity and quality assessments. Total RNA was treated with DNase I to degrade DNA contamination, if any. Library preparation was done using the Integrated DNA Technologies (IDT) xGen RNA library preparation kit with the NEB polyA selection module. The preparation is performed according to the manufacturer's instructions. Briefly, it starts with RNA fragmentation, followed by random priming and reverse transcription to generate first-strand cDNA. This follows by tailing and adapter ligation to the 3-end of the cDNA molecule. The final step is the PCR to increase library yield. Sequencing was performed at the Oklahoma Medical Research Foundation NGS Core, USA.