RNA-Seq of Seriola rivoliana: fertilized good eggs1
Total RNA extraction was performed using Tripure and treated with Turbo DNA-free kit. Integrity was determined by electrophoresis in a 1% chlorine-treated agarose gel, and by Agilent 2100 Bioanalyzer. Transcriptome libraries were constructed using NEBNext Ultra IITM RNA Library Prep Kit for Illumina. After high-temperature fragmentation with magnesium ions, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for a directional library. The cDNA was end-repaired for blunt ends, followed by adding an "A" overhang at both ends of the cDNA to perform adapter ligation, size selection, dUTP enzyme digestion, PCR amplification, purification, quality control, and concentration. The libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, Inc., San Francisco, CA, USA) and paired-end reads (Pair-End 150) were generated. The amount of sequencing data for each library was 12 GB. Clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from raw data (Phred quality score Q < 20). At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on clean, high-quality data. Differential expression: poor eggs vs good eggs. See Guerrero-Tortolero and Campos-Ramos. (In Press, 2025). Aquaculture