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However, when YRY triplex formation was discouraged by conducting reactions at pH 9.0, there was less bias in the insertion location (Figure 3).
This strategy is based on the assumption that there is no bias in the insertion site of a HTgene with respect to the neighboring genes in the receiving (pox) genome.
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As shown in Figure 3 figure supplement 3, the read depth varied somewhat along the primary sequence, presumably due to known weak biases in the insertion sites for the Nextera transposon (Adey et al., 2010).
There was no bias in the orientation of insertion as 691 sense and 707 anti-sense IAPLTR1_Mm elements were identified throughout the genome.
Based on this we conclude that the Selected set has no significant bias in the distribution of insertions in the genome compared to whole P{EP} and P{EPgy2} sets.
The added value of the whole genome resequencing has included a characterization of SNP distribution, the identification of unexpected nonsense mutations, and has revealed the strong bias in the size of insertions and deletions relative to their location in coding vs. non-coding sequence.
There could also be a bias for the insertion of retrogenes in the same regions where retroelements insert given that they are known to use the same machinery [ 28] or for both of them to insert in open chromatin, inserting thereby in the same regions [ 29].
Whether this was due to bias in transposon insertion or due to sampling variance is yet to be determined.
Random gene disruption strains were generated using a mini-Tn 10 transposon derivative having reduced bias in potential insertion sites [ 41].
In total we identified 127 inserts at unique locations in the genome (Additional file 1 Table S1) and we have not identified any insert at the same location from two different parent populations, suggesting that there is no strong bias in preferred insertion sites between different experiments.
Such A-rich regions are preferred targets for insertions [ 5, 19] and can bias the insertion profile.
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