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. Author manuscript; available in PMC: 2019 Oct 19.
Published in final edited form as: J Mol Biol. 2018 Sep 1;430(21):4307–4324. doi: 10.1016/j.jmb.2018.08.025

Table 1.

Description of primer sets used for the selective amplification of different MMTV and host transcripts.

Target mRNAs Primer Set Used and its Description
All MMTV mRNAs from the LTR promoter, including gRNA. OTR671(+)/OTR672(−). Binds within 5’ R/PBS.
All MMTV spliced mRNAs except gRNA due to long length. OFM112(+)/OFM114(−). Binds within 5’ U5 and 3’ U3 flanking the genome.
MMTV gRNA only. OFM112(+)/OFM113(−). Binds a region flanking SD1 (5’ U5 and Gag ORF)
MMTV spliced mRNAs from the LTR promoter. OFM112(+)/OFM114(−). Binds within 5’ U5 and 3’ U3 flanking the genome.
MMTV spliced mRNAs from the Env promoter. OFM115(+)/OFM114(−). Binds downstream of SD2 and 3’ U3 region.
All MMTV mRNAs, both spliced and unspliced. graphic file with name nihms-1505768-t0009.jpg Taqman assay 1 (T1). Binds within 5’ U5 (nt 1192- _ 1259) and can detect a minimum transcript size of 86 nt.
Unspliced MMTV gRNA only. graphic file with name nihms-1505768-t0010.jpg Taqman assay 2 (T2). Binds within gag, 270 nt 3’ from SD1 (nt 1729–1791) and can detect a minimum transcript size of 618 nt.
GAPDH host mRNA. ORT581(+)/OTR582(−). Detects host gapdh gene or mRNA.
Spliced β-actin mRNA. OTR580(+)/OTR581(−). Detects spliced β-actin mRNA.
Unspliced β-actin mRNA. OTR582(+)/OTR581(−). Detects unspliced β-actin gene or mRNA.