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Total nucleic acids were subjected to Dnase treatment and the remaining total RNA was used as template for random hexamer-primed reverse transcription performed independently at 37°C and 50°C, respectively.
For qRT PCR quantification, 1 μg of RNA was used as template for random hexamer cDNA synthesis (Invitrogen) using Superscript (200 U/μl) (Invitrogen) according to supplier's protocol.
The template for random priming was a dh repeat PCR product amplified from genomic DNA with the dhH-siRNA and Cen-dh-FOR2 primers.
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After chemically reversing the Dynabead binding, the RNA was denatured and used as template for random-primed cDNA synthesis.
RNA was extracted from tissues using TRIzol (Invitrogen), DNAse-treated and used as a template for random-primed cDNA synthesis with Superscript III (Invitrogen).
The resulting RNA is denatured and used as template for random-primed cDNA synthesis then end repaired withT4 DNA polymerase, Klenow polymerase and dNTPs.
Polyadenylated RNA was isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA), denatured, and used as a template for random-primed cDNA synthesis and end-repair with T4 DNA polymerase, Klenow polymerase and dNTPs.
Subsequently, mRNA was fragmented to short fragments to be used as templates for random hexamer-primed synthesis of first-strand cDNA by fragmentation buffer.
Fragmentation buffer was added and the resulting 200~300 bp fragments were used as templates for random hexamer-primer synthesis of first-strand cDNAs.
Templates for random primer labeling were amplified from genomic DNA of N402 using the following primer pairs: actA (An15g00560): 5'-atctcccgtgtcgacatgg-3' and 5'-gcggtggacgatcgagg-3'; nagA (An09g02240): 5'-cccgcgcgaggtatattcac-3' and 5'-cctgggcgtcagtcagattt-3'; brlA (An01g10540): 5'-ggtaacatgtccgatcgcctg-3' and 5'-gcaactttcctggagggctg-3'.
To overcome the challenge of probe design for templates of random sequence, we adapted the universal template (UT) approach where a probe-binding sequence is appended to one of the PCR primers [ 10].
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