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| 72°C for 0.5 4 min. (depending upon template length), and 1x 72°C for 3 min. Samples were electrophoresed on 1.7 % TAE agarose gels plus 0.01 % SyberSafe stain (Invitrogen).
The relationship between template length and sequence frequency was determined.
A correlation between amplified template length and droplet fluorescence amplitude has previously been reported in the context of TaqMan probe-based next-generation sequencing library characterization but not in the context of a single-color binding dye.
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We employed a 120 min RT incubation time in this protocol after multiple experiments, and since the excess extension time may compromise yield and specificity, the optimal PCR extension time was determined based on template lengths and extension rates of the DNA polymerase.
However, the DNA polymerase was identified as the primary source of bias with a variety of commercially available DNA polymerases skewing the amplification profile of the Neandertal genome with regard to GC content and template length [ 5].
Relative gene expression was calculated as: number of copies (NC) = (A × 6.022 × 10)/(B × 1 × 109 × 650 kDa), where A is the template quantity (ng of vector plus insert), B the template length (bp vector plus insert), and 650 kDa is the average weight of a base pair according to [ 58].
CCS allows for the repeated sequencing of individual inserts and, depending on template length, stochastic sequencing errors are reduced with each CCS pass [ 16, 17].
We established these criteria because in our topological-mapping approach, it is the average relative position to the NM anchoring point and not the actual template length the critical parameter that determines the average sensitivity to DNase I of each sequence mapped.
In this approach, template length (L M ) is a key parameter.
A very small template length makes results sensitive to noise while a very large length reduces detection precision.
To determine if part of the increased termination was simply due to the increased template length, we inserted several kilobases of heterologous coding sequence downstream of each poly(A) region test fragment.
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