Transcriptome Sequencing and Targeted Amplicon

Previously isolated mRNA was prepared for transcriptome sequencing using the TruSeq Stranded mRNA, HT kit (Illumina, San Diego, CA) following the High Sample (HS) protocol. Prepared samples were quantified and checked for quality, then pooled in equimolar concentrations. Library pools were loaded into an Illumina High Output NextSeq 2 × 150bp kit, according to manufacturer recommendations for sequencing on the Illumina NextSeq 550 platform. The transcriptomes were assembled with metaSPAdes (85 (link)) using default settings. For targeted amplicon studies, complementary DNA (cDNA) was generated with the SuperScript IV VILO RT-PCR Master Mix with ezDNase enzyme (Invitrogen, Carlsbad, California), following manufacturer's recommendations.