RNA-Seq of  VHSV: plaque
Viral RNA was isolated from 140 ml of concentrated virus using the QIAamp Viral RNA Mini kit (Qiagen) and then subject to retrotranscription with the SuperScript III Reverse Transcriptase (Invitrogen). Double-stranded cDNA was synthesized using NEBNext mRNA Second Strand Synthesis Module (Euroclone), purified with MagSI-NGSPREP PLUS beads (MagnaMedics) and quantified with Qubit dsDNA HS assay kit (Thermo Fisher). The cDNA library was prepared using Illumina Nextera XT DNA Sample Preparation kit (Illumina), and fragments were selected with MagSI-NGSPREP PLUS beads (MagnaMedics). Library was checked for quality and size with Agilent 2100 Bioanalyzer (Agilent High Sensitivity DNA kit, Agilent Technologies).