title: RNA-seq of Ginglymostoma cirratum: healthy male liver
design: Before library construction, all samples passed through three steps to ensure quality: 1) RNA degradation and contamination was monitored on a 1% agarose gel, 2) RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), and 3) RNA integrity and quantitation was assessed using the RNA Nano 6000 Assay kit of the Agilent Bionanalyzer 2100 System (Agilent Technologies, CA, USA). A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturers recommendations, and index codes were added to attribute sequences to each sample.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to manufacturers instructions.  After cluster generation, the libraries were fed into Illumina machines according to their activity and expected data volume, and paired-end reads were generated. The original raw data from Illumina were transformed to Sequence Reads by base-calling.  Raw data were recorded as a FASTQ file.  The error rate for each base was calculated.  Error rate increases as the sequencing reads are extended and sequencing reagents become increasingly scarce.  Raw reads were filtered to remove reads containing adapters or reads of low quality.