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The conditions for the second step mixture were identical to those for the primary PCR, with the exception of the template amount (i.e. 4 µl of a 1/10 dilution of the primary B1 PCR product, determined to be optimal).
They were prepared as separate samples where aliquots of sterile water were added to master mix and contained every reagent with the exception of the template DNA.
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With the exception of the primer-template, reaction components were identical to the PAGE-analyzed reactions.
An exception is the template of Bonifacio and Borba.
Expression of Bax and Bcl-2 levels was determined by quantitative real-time PCR (7500 Real-Time PCR System, Applied Biosystems, USA) on cDNA samples using Cyber Green Master Mix (ROVALAB, Germany) with the exception of template and primers.
The negative control was placed with the same reagents as those used with actual samples, with the exception of DNA templates.
Reactions contained 400 ng of template RNA with the exception of the 28S-specific reactions, which contained 5 ng of template RNA.
The number of amplifiable copies of the p14 and COL2A1 genomic regions detected by MSRE-dPCR, mock digestion conditions and MethyLight dPCR was less than the values based on Qubit analysis (p < 0.05) with the exception of the MDRE dPCR assay (0% methylated template (p = not significant)).
Default parameters in Modeller were applied, excluding water molecules and any ions that were part of any of the templates with the exception of the heme and heme iron.
With the exception of the V6 region, the average candidate sequence found a template sequence that was between 3.7 and 7.5% different from the optimal template when using kmer searching; the V6 candidates averaged a difference of 12.5% from their optimal template.
With the exception of the V6 region, the average candidate sequence found a template sequence that was between 7 and 17% different from the optimal template when using suffix tree searching; the V6 candidates averaged a difference of 37% from their optimal template.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com