Illumina deep sequencing reads corresponding to XMRV from the VP62, VP35, and VP42 prostate cancer sample and an XMRV-infected LnCaP cell line
For the XMRV-positive and XMRV-negative prostate cancer samples, randomly amplified cDNA was prepared for deep sequencing using a variation of Illumina’s TruSeq protocol (Illumina) as previously described [2,42].  Briefly, amplified cDNA samples were cleaned using AMPure SPRI beads (Agencourt AMPure XP) and digested using the restriction enzyme BpmI (New England Biolabs, Ipswich, MA) for 2 hr at 37°C, followed by end-repair and A-tailing with Klenow and Taq polymerase, respectively (Invitrogen).  Size selection for ~250 base pair (bp) fragments was then performed using AMPure beads, and sequencing adaptors containing 6-nucleotide barcode tags were attached according to an Illumina paired-end protocol.  For the 22Rv1 and LNCaP cell lines, the Illumina ScriptSeq v.2 kit (Illumina) was used for library generation according to the manufacturer’s instructions.  Final libraries were analyzed using the Bioanalyzer DNA 12000 chip for assessing size distribution (Agilent) and SYBR©FAST qPCR for confirming properly adapted DNA fragments (KAPA Biosystems).   Either 100 bp or 150 bp paired-end resequencing was then performed using Illumina HiSeq or MiSeq instruments, respectively.