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These RNAs were not observed when reactions were performed using a control template carrying disruptive base-pair substitutions within the transcribed-region −10-like element.
Furthermore, the ∼35-nt pause RNA was barely detected with or without excess σ using a control template carrying base-pair substitutions that disrupt sequence-specific recognition of the transcribed-region −10-like element by σ region 2 (Deighan et al., 2011).
We will further demonstrate the superiority of a correlation treatment over more conventional ones, using a control template (reference image) and the signal image to determine resonance shifts down to Δ m~0.005, thus equivalent to such a subnanometer RWG pattern variation.
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M13mp18ss circular DNA (NEB) was used as a control template for Φ29 activity as described (Henson et al, 2009).
A RP23-92N4 (CHORI; BACPAC) Bacterial Artificial Chromosome (BAC) clone covering the Pou3f3-Dali locus was treated as above and used as a control template for the 3C assay.
Genomic DNA was used as a control template in parallel PCR reactions to confirm the expected electrophoretic pattern of the retroposed sequences.
Plasmid pTRI-Xef, used as a control template containing 1.85-kbp elongation factor 1-α gene from Xenopus laevis (EF-1α), was already linearized by Ambion (Austin, Texas, USA).
Using a control non-G4 plasmid template, we observed the accumulation of ∼3,000-nt ∼3,000-ntlinears, corresponding to fully replicated nicked molecules, and slower migrating supercorrespondingles from 10 min onwards (Fig C, leftopanel).
Relative values were calculated by comparing the average C t values from each sample against a standard curve generated using a TSR8 control template.
The standard curve was generated by performing serial dilutions of the armored HIV RNA and assaying each dilution twice per RT enzyme, while using a non-template control in each assay to check for contamination.
Quantitative values of the telomerase activity were obtained from a standard curve generated by using dilutions of control template provided by the kit.
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