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Techniques like QMC-PCR that mitigate variation in template quantity and quality could simplify DNA isolation from large plant populations.
Variation in template copy number among pooled genotypes can be compensated for by deeper sequencing, imputation of missing data, or by rerunning samples sequenced at low depth.
If there is wide variation in template selection and also important differences in the templates, then future refinements of the system would need to consider selection of the template as an important factor in optimizing its effects.
For some experiments, semi-quantitative reverse transcription PCR (semi-q-RT-PCR) was performed on cDNAs, where we used HvGAP amplification (Additional file 5: Table S3) to indicate between-sample variation in template concentration.
Additionally, the cases and controls used in the study by Field et al. were extracted using different techniques potentially introducing variation in template quality as a contributor to the poor performance of real-time QPCR.
Importantly, the same DG markers were sequenced consistently at high or low relative frequencies from different RILs, indicating that variation in depth of sequencing was intrinsic to the DG template rather than a result of random variation or due to variation in template preparation.
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The requirement of the Fluidigm Access Array system for high template amounts and its sensitivity to variations in template quality rendered it unsuitable for bisulfite PCR applications utilizing FFPE DNA.
Regions with large variability within an ensemble of theoretical models often reflect segments, which cannot be predicted with high confidence, e.g. due to the variation in alternative template structures, flexible loop regions or unaligned regions (indels) in the target-template alignment (42).
Here, we estimated the rate of base misincorporation of a widely-used PCR-cloning method, using a single copy mitochondrial gene from a single individual to minimise variation in the template DNA, as 1.62×10−3 errors per site, or 9.26×10−5 per site per duplication.
Variation in DG template length also affects the relative frequency of read acquisition on the Illumina GAIIx platform.
The raw data were analyzed with the LightCycler software, (LightCycler 480, Software 1.5) and transcript levels were normalized to actin to minimize variation in cDNA template levels.
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