Table S1. Primers used for qPCR qPCR primer Sequence - Plos

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MALAT1 F-GACGGAGGTTGAGATGAAGC. R-ATTCGGGGCTCTGTAGTCCT. Tripathi et al., PLOS Genetics,. 2013. GusB. F- CTCATTTGGAATTTTGCCGATT.
Table S1. Primers used for qPCR qPCR primer GFP DsRed 18S rRNA 47S rRNA RPS18 RPS6 Beta-actin GAPDH POLR2A 7SK 7SL 5S U2 MALAT1 GusB EEF1A Betatubulin GAPDH – intronic Beta-actin intronic

Sequence (5’-3’)

source

F- CAACAGCCACAACGTCTATATCATG R- ATGTTGTGGCGGATCTTGAAG F-GATCCACAAGGCCCTGAAGC R-GCTCCACGATGGTGTAGTCC F- GTAACCCGTTGAACCCCATT R- CCATCCAATCGGTAGTAGCG F- TGTCAGGCGTTCTCGTCTC R- AGCACGACGTCACCACATC F- GAT GGGCGGCGGAAAATAG R- GCGTGGATTCTGCATAATGGT F- CGATGAACGCAAACTTCGTA R- TTCGGACCACATAACCCTTC F- CGTCACCAACTGGGACGACA R- CGTCACCAACTGGGACGACA F- AGCCACATCGCTCAGACAC R- TGGAAGATGGTGATGGGATT F- GAGAGTCCAGTTCGGAGTCCT R- CCCTCAGTCGTCTCTGGGTA F- CTCCAAACAAGCTCTCAAGGTCCA R- ATGCAGCGCCTCATTTGGATGTGT F- GGAGTTCTGGGCTGTAGTGC R- GGAGTTCTGGGCTGTAGTGC F-GGCCATACCACCCTGAACGC R-CAGCACCCGGTATTCCCAGG F- TGGAGCAGGGAGATGGAATA R- CGTTCCTGGAGGTACTGCAA F-GACGGAGGTTGAGATGAAGC R-ATTCGGGGCTCTGTAGTCCT F- CTCATTTGGAATTTTGCCGATT R- CCGAGTGAAGATCCCCTTTTTA F- TGTCGTCATTGGACACGTAGA R- ACGCTCAGCTTTCAGTTTATCC F- TCTACCTCCCTCACTCAGCT R- CCAGAGTCAGGGGTGTTCAT F- TCCCCTCCTCATGCCTTCTT R- CCAGGCGCCCAATACG F- AGGGCTTCTTGTCCTTTCCT R- CATAGGAATCCTTCTGACCCA

Lee and Glaunsinger, PLOS Biology, 2009 Janus et al., Appl Env Microbiology, 2007 Abernathy et al., Cell Host Microbe, 2015 Feng et al., Nat Struct Mol Biol, 2010 Mak et al., Biochemistry Research International, 2011 Hagner et al., Oncogene, 2011 Feng et al., Nat Struct Mol Biol, 2010 Arias et al., PLOS Pathogens, 2014 Farrall et al., Oncogene, 2009 Barboric et al., PNAS, 2009 Ren et al., PLOS ONE, 2012 Thomas et al., Cell Reports, 2015 Thomas et al., Cell Reports, 2015 Tripathi et al., PLOS Genetics, 2013 Abernathy et al., Cell Host Microbe, 2015 Abernathy et al., Cell Host Microbe, 2015 This paper Sei et al., PLOS Pathogens, 2015 Sei et al., PLOS Pathogens, 2015

HIST1H3C

F- GCTTGCTACTAAAGCAGCCC R- AGCGCACAGATTGGTGTCTTC

PR8 PA-X

F-GCGACAATGCTTCAATCCGA R-TTGACTCGCCTTGCTCATTG F- ATGGAAGACGCCAAAAACAT R- GCCTTATGCAGTTGCTCTCC F-ACGAAGGTACCCAACCCTCT R-GGTGTAAGTGTTCGCCTGGT F-TCTCAGCGGTCCAAATTCCT R-TCTGCCAGTACTTGCTTCCA F- CCCAGGATGTGCTCTCTGAT R- TTCGTCCATTCTCACCCCTC F- TTTGGCCTGGTATGTGCAAC R- ACCATTTGCCTAGCCTGACT F- GGTCGAAACGCCTATCAGAA R- ACTTTGGCACTCCTTCCGTA F- CTGTGTCAAGCTTTCAGGTAGA R- GGTACAGAGGCCATGGTCAT F- CTGTGTCAAGCTTTCAGGACA R- TTGTTCCCGCCATTTCTC

Luciferase TP53TG1 PR8 PA PR8 NP PR8 M1 PR8 M2 PR8 NS1 PR8 NEP

Harvard primer bank ID 21071022c1; Spandidos et al., 2010 This paper This paper Yang et al., PLOS ONE, 2013 This paper This paper This paper This paper This paper This paper