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The primers used in the first strand synthesis and the PCR amplification are listed in Additional file 1: Table S2.
The primers used in the first strand synthesis were cDNA 3′ SMART CDS Primer II A, 5′-AAGCAGTGGTATCAACGCAGAGTACT (30) VN-3′ (N = A, C, G or T; V = A, G or C), and SMART II A oligonucleotide, 5′-A AGCAGTGGTATCAACGCAGAGTACGCGGG-3′.
We assumed that the precise sequence of the T7 primer is important in this respect because the complete T7-primer is incorporated in the first strand cDNA generated by an RT enzyme upon annealing to the poly-A tail of mRNA extracted from samples.
Furthermore, we found by substituting T7-Oligo dT primers for T7N6 in the first strand synthesis in the ANRO process that about 20% of the biotinylated NRO material was already polyadenylated (data not shown), indicating rapid processing of primary transcripts to mature mRNAs.
cDNA synthesis was initiated using an oligo (dT) primer, using methylated C in the first strand synthesis reaction.
Briefly, total RNA (5 μg) was reverse transcribed using T7-Oligo (dT) primer in the first strand cDNA synthesis.
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Minus RT control reactions were done by synthesizing the first strand in the absence of StrataScript enzyme.
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