RNAseq of Astyanax:Dark adapted
Total RNA was isolated from samples stored in TRIzol reagent according to the manufacturers instructions (Invitrogen, Carlsbad, CA, USA). The fragment size, concentration, RNA integrity number (RIN) and 28S/18S ratio of RNA extracts were determined using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The cDNA libraries were constructed using TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Fragment sizes and concentrations of libraries were verified using an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR machine (Thermo Fisher Scientific, Waltham, MA, USA). The samples were sequenced in a single Hiseq X-ten lane with a strategy of 150 bp paired-ends (PE), resulting in about 8 Gb raw data for each sample. To avoid potential adapter contamination, the last 60 bp of all reads were trimmed. Subsequently, the reads were removed if they contained: 1) more than 50% low quality (Q<35) bases; 2) more than 10 Ns, and 3) were PCR duplications. Cleaned read quality was confirmed in FASTQC [54], and a total of 230,437,086 cleaned reads were retained for transcriptomic analysis.