Detecting Cellular and EBV Transcripts

Total RNA was extracted using TRIzol (Thermofisher). For detection of cellular or EBV transcripts, RNA was DNAse-treated and reversed transcribed using MultiScribe (Thermofisher) with random hexamers. Transcripts were detected using SYBR Green qPCR and oligonucleotides designed to amplify gene specific regions of ~200 bp. Primers for amplification of EBV transcripts BZLF1, BRLF1, BALF4, BNLF2a, and BHRF1 are described in [81 (link)]. Oligonucleotides are listed in Table S1. miRNAs were detected using commercial Taqman assays or miRNA stem-loop qRT-PCR assays as previously described [11 ,49 (link)]. miRNA levels are reported relative to miR-16 (assay #000391, Thermofisher) or U6 (assay #001973, Thermofisher) as indicated. All PCR reactions were performed in technical replicates (duplicates or triplicates).