title: RNA-seq of Amphilophus citrinellus scales of dark and gold morph
design: RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturers protocol. Briefly, 1g RNA was put into mRNA selection by poly-T oligo attached magnetic beads followed by fragmentation (94C for 6 min). The cleaved mRNA fragments were reverse-transcribed into first strand cDNA using GoScript Reverse Transcriptase (Promega) and random hexamer primers (Illumina). We used Illumina-supplied consumables to synthesize second strand cDNA following by adenylating 3 ends. Barcoded adapters from TruSeq RNA CD Index Plate (Illumina) were ligated to the ends of the double strand cDNA. The final libraries were amplified using 15 PCR cycles and quantified and quality-assessed using an Agilent DNA 12000 Kit on a 2100 Bioanalyzer (Agilent). Indexed DNA libraries were normalized. Libraries were sequenced on a HiSeq X Ten platform (BGI Genomics, Beijing). We obtained between 13 and 45 million reads per sample (average: 31 million reads).