Porcine Transcriptome Analysis via Ribo-Zero and Illumina Sequencing

Total RNA was divided into two samples after preparation. In one sample, ribosomal RNA was removed by Epicenter Ribo-zero™ rRNA Removal Kit (Epicenter, Madison, WI, USA), and residual RNAs were cleaned by ethanol precipitation. The sequencing libraries were generated using rRNA-depleted RNA with a NEB Next® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA). The constructed libraries were evaluated on an Agilent Bioanalyzer 2100 system (12 (link)). RNA integrity was checked by microcapillary electrophoresis using an Agilent 2100 Bioanalyzer with an RNA 6000 Nanochip kit (Agilent Technologies, Germany) (15 (link)). Sequencing was then performed using a paired-end 125-cycle rapid run on an Illumina HiSeq2500 (Illumina Inc., San Diego, CA, USA). Low-quality reads were removed, and the clean reads were filtered from the raw reads and mapped to the porcine reference genome (Sus scrofa v10.2). The mapped reads for each sample were independently assembled using Cufflinks (v2.1.1).