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 following the protocol for the Illumina TruSeq Stranded mRNA Preparation Kit, but without the polyA enrichment step.  Briefly, 100 ng of RNA extracted from Virus#3 was chemically fragmented and reverse-transcribed into cDNAs.  Double strand cDNAs were adenylated at the 3ends and individually indexed, followed by 15 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), pooled with 12 other individually indexes samples and subjected to paired-end sequencing (100 x 2 cycles) on an Illumina HiSeq 2500 sequencer in one lane of a rapid run flow cell.