RNA-Seq of Sus scrofa stool
Nucleic acid extractions were performed using the PowerFecal DNA/RNAPurification Kit (QIAGEN), following manufacturers instructions. All extracts wereQC'ed using fluorimetry (Qubit) and TapeStation (Agilent).36 RNA samples were used to generate RNA-Seq libraries using the TruSeq RNA LibraryPrep kit and the Ribo-Zero Plus Microbiome rRNA Depletion Kit (Illumina), following themanufacturer's guidelines. All libraries were combined in equimolar concentration and loaded, along with 1% PhiX,into S4 flow cell lanes for clustering. The sequencing was performed using a 318 cyclespaired-end run on the NovaSeq 6000 instrument to generate 150 bp paired-end reads.