RNA-Seq of recombinant Mumps virus
Cell culture supernatant was treated with micrococcal nuclease (New England Biolabs), prior to RNA extraction. Viral RNA was extracted using the QIAamp MinElute Virus spin kit (Qiagen) and eluted in 25 l of DEPC treated water.  This RNA was processed using the NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs).  Briefly, 100 ng of RNA extracted from virus r88+JL(M/F/SH/HN) was chemically fragmented and reverse-transcribed into cDNAs.  Double strand cDNAs were adenylated at the 3 ends and individually indexed, followed by 12 cycles of amplification and then purified using Agencourt AMPure magentic beads (Beckman Coulter).  cDNA libraries were checked for size and quality using a BioAnalyser (Agilent Technologies) and subjected to paired-end sequencing (250 x 2 cycles) on an Illumina MiSeq.