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DNA samples of pooled transposants are sheared and amplified in multiple phases so as to enrich for Dsg elements and their adjacent insertion sites for high throughput NGS.
The negative correlation between adjacent insertion ratio is not surprising since the calculation uses the same exon length as dividend (equation (5)) but with opposite signs.
The position of the enhanced tCUP4 promoter at the right border reduced the likelihood of promoter interactions with sequences within the adjacent insertion site.
The expression pattern of SBLac[-15] was shown to reflect that of the Shh pattern within the CNS, gut and limbs; however, levels were appreciably lower than the adjacent insertion, SBLac[-3].
We marked CEN5 by the adjacent insertion of a tet operator array bound by TetR-3CFP (cyan fluorescent protein) and CEN15 by a lac operator array bound by GFP-lacI [21].
CEN3 was visualized by adjacent insertion of a tet operator array that was bound by Tet repressors fused with green fluorescent protein (GFP) [10], and therefore CEN3 was visualized as a small GFP dot.
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Thereby the correlation in the formation of adjacent insertions or deletions is taken into account.
Third, their non-adjacent insertion ratios are more negatively correlated as shown in Figure 5.
Results in Additional file 1: Figure S9 suggest that intron loss might account for increasing σ x, and more negative correlation between non-adjacent insertion ratios.
For loci containing adjacent independent insertion events, the independent insertions were treated as independent markers.
The sequencing verification recovered 11 loci that contained adjacent independent insertion events (i.e. independent insertions in different species that are within sufficiently close genomic proximity to be amplified by a single set of PCR primers; see Discussion for details).
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