Table 1.

Primers used to create probes for detection of genomic and antigenomic RNA transcripts from the SYNV minireplicon

Clone name	Directiona	Primer name	Primer sequence	Purpose
T7rsGFP	F	T7rsGFPF	TAATACGACTCACTATAGGCGGAGAAGAACTTTTCACTGG	To amplify a plus-sense rsGFP probe for detection of minus-sense transcripts harboring rsGFP
	R	3GFP	TTAGTATAGTTCATCCAT
rsGFPT7	F	5GFP	ATGGGTAAAGGAGAAGAAC	To amplify a minus-sense rsGFP probe to detect plus-sense rsGFP transcripts
	R	T7rsGFPR	AATACGACTCACTATAGGCCCCAGCAGCTGTTACAAAC
T7MR	F	T7F	TAATACGACTCACTATAGGCAGAGACAGAAACTCAGAAAATACAATCACCG	Template to create a size marker to assess mobility of minus-sense MR transcripts
	R	rev	TTATACTTCAAGAGATATAGATGTACACAATTTCCTGGAAG
MRT7	F	sense	AGAGACAGAAACTCAGAAAATACAATCACCG	Template to create a size marker standard for the plus-sense MR transcript
	R	T7	TAATACGACTCACTATAGGCAGAGACAAAAGCTCAGAACAATCCC
	F	rz sense	GTCTCTCTGATGAGGCCGAAAGGCCGAAAACCCGGTATCCCGGGTTC	To amplify the leader probe transcription template
	R	N5′UTR R	ATGCTAGCGATTACCTGCAATTAAAATAC
for positive-sense	R	rev	TTTTTCTTTAATCTACTAATCAGTTAAAATCAC	To amplify genomic probes for detection of the leader RNA and full-length antigenomic RNAs
for negative-sense	F	sense	AGAGACAGAAACTCAGAAAATACAATCACCG	To detect full-length genomic transcript with the plus-sense leader probe
CAT	F	NPJF	ACTACAGCCACAACTCTACC	Template to prepare the CAT probe
	R	L3′mRNAR	TTTTTCTTATACTTTCAAGAGATATAG
CAT for positive sense	R	L3′mRNAR	TTTTTCTTATACTTTCAAGAGATATAG	To detect antigenomic CAT transcript
	F	sense	ATCGCTAGCTGGCCATGTACATCTATATCTCTTGAA	Template to prepare the trailer probe
	R	SYNV R	AGAGACAAAAGCTCAGAACAATCCC
Trailer for negative sense	F	sense	ATCGCTAGCTGGCCATGTACATCTATATCTCTTGAA	To synthesize a trailer probe for detection of genomic RNAs
RT-PCR
Reverse transcription	F	sense	AGAGACAGAAACTCAGAAAATACAATCACCG	To make a genomic sense cDNA template
PCR	F	5eGFP-NheI	GCTAGCATGGTGAGCAAGGGCGAGGAG	For amplification of minus-sense eGFP genomic transcripts
	R	3eGFP-NPJ	GTAGAGTTGTGGCTGTAGTTTATTACTTGTACAGCTCGTCCAT

^aF, forward; R, reverse.