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Due to this difference in the energy distribution ratio, the physical range of damage fragments through the sensitive microvolume of the detector will also be different, because inelastic reactions result in a much greater variance in the range of fragments in the silicon, compared to elastic damage which is uniformly distributed throughout.
The size of contigs assembled from the paired-end reads is dependent on the size range of fragments selected during library construction.
We designed a new polylinker which allows for the bidirectional cloning of a wide range of fragments.
DNA was sheared with an S2 focused-ultrasonicator (Covaris, Woburn, MA) to achieve a target size range of fragments of 100 900 bp.
Sequencing adaptors were then ligated to the fragments, and agarose gel electrophoresis used to select the range of fragments suitable for PCR amplification.
In muscle nuclei, the flanking nucleosomes were also present, and protected a very similar size range of fragments as in the total nuclei sample.
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Additionally this fragmentation is potentiated to support widely range of fragment ions which can cover the location of mutation.
We investigate whether amphibian diversity is affected by patch size in the largest study (in terms of number of fragments and range of fragment sizes) ever conducted in tropical forests.
A possible reason is that the scale at which previous studies were conducted was too small (only few forest fragments and/or a small range of fragment sizes considered) and/or the sampling method was not the most optimal one.
Varying the gel agarose content achieves better resolution only for a limited range of fragment sizes, with the trade-off of worsening the resolution in other size ranges.
To allow for a wide range of fragment sizes, we chose a GATC overhang for our splinkerette oligonucleotide design (Figure 1C; Splinkerette Protocol S1).
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