Table 1.

Oligonucleotide sequences.

RNA oligos for SL-qPCR validation
Mm pre-tRNA-Tyr	5’ rUrArUrCrUrCrCrCrUrUrCrGrArUrArGrCrUrCrArGrUrUrGrGrUrArGrArGrCrGrGrArGrGrArCrUrGrUrArGrUrArUrArGrGrUrGrUrUrGrArUrArUrCrCrUrUrArGrGrUrCrGrCrUrGrGrUrUrCrGrArArU
Mm 5’ pre-tDR-Tyr	5’ rUrArUrCrUrCrCrCrUrUrCrGrArUrArGrCrUrCrArGrUrUrGrGrUrArGrArGrCrGrGrArGrGrArCrUrGrUrArG
Northern probes
Mm-tRNA-Tyr-GTA-1-3_probe	5’-CTACAGTCCTCCGCTCTACCA
5S_probe	5’-AGCCTACAGCACCCGGTATT
Primers used for reverse transcription
5’tDR-Arg-TCT-3-1_RT	5’-CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTAGAAGTC
5’tDR-Gln-CTG_RT	5’-CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTGCTAACC
5’tDR-Leu-CAG-3_RT	5’-CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCTTAGA
5’tDR-Tyr-GTA-1-3_RT	5’-CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTACAGTC
Primers used for qPCR
Mm-tRNA-Tyr-GTA-1-3_qPCRf	5’-CCTTCGATAGCTCAGTTGGTAGAGC
Mm-tRNA-Tyr-GTA-1-3_qPCRr	5’-GGATTCGAACCAGCGACCTAAGGATATC
5’tDR-Arg_TCT-3-1_qPCRf	5’- GGCTCTGTGGCGCAATGG
5’tDR-Gln-CTG_qPCRf	5’- GGTTCCATGGTGTAATGGT
5’tDR-Leu-CAG-3_qPCRf	5’-GTCAGGATGGCCGAGTGG
5’tDR-Tyr-GTA-1-3_qPCRf	5’-CCTTCGATAGCTCAGTTGGTAGAGC
SL-univ_qPCRr	5’-GTGTCGTGGAGTCGGC
Mm_Clp1_qPCRf	5’-ATGAGCGAGGAATCCAATGATG
Mm_Clp1_qPCRr	5’-CTCCAACTGAACCGATTGAGAG
Mm_Tsen2_qPCRf	5’-CCAAACTTCACAATCGCCAAC
Mm_Tsen2_qPCRr	5’-AGTGGCTCTGTGTAGTCTGTAA
MHV68_Orf50_qPCRf	5’-GGCCGCAGACATTTAATGAC
MHV68_Orf50_qPCRr	5’-GCCTCAACTTCTCTGGATATGCC
MHV68_gB_qPCRf	5’-GGCCCAAATTCAATTTGCCT
MHV68_gB_qPCRr	5’-CCCTGGACAACTCCTCAAGC
18S_qPCRf	5’-GTGGAGCGATTTGTCTGGTT
18S_qPCRr	5’-CGCTGAGCCAGTCAGTGTAG