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In the most ideal situation where hybridization is determined solely by sequence complementarity, a designed probe would either consistently hybridize if the assumed target orientation is correct or not hybridize at all if wrong.
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We have recently shown that GSCs with misoriented centrosomes do not enter mitosis until the orientation is corrected, pointing to the presence of a novel checkpoint that monitors centrosome orientation ("the centrosome orientation checkpoint") [21].
This inside-out orientation is corrected as the embryo turns itself right-side out during inversion.
The construct was sequenced to ensure that the sequence and orientation were correct.
Cutting with BamHI and KpnI confirmed that the construct orientation was correct.
The supervisor recorded whether these adjustments were asked for and whether the probe orientation was correct, by checking the position of the orientation marker.
Compass readings of the sample orientation were corrected for the locality declination of the present-day Earth's magnetic field of 7°, calculated using the 12th International Geomagnetic Reference Field (Thébault et al. 2015; http://wdc.kugi.kyoto-u.ac.jp/igrf/point/index-j.html).
Before the hardening reaction had been completed the extrudate orientation was corrected to get the fracture surface as horizontal as possible.
Using these parameters, reads were only aligned when their relative orientations are correct and their inferred distance along the assembly (the aligned span size) was consistent with the estimated library insert size.
The latter is most useful for coregistration with a preoperative fractional anisotropy map, which carries with it the representation of a tractographic representation of, for example, the optic radiation, which is then warped into an orientation that is corrected for the brain shift that occurs through the surgery (Daga et al., 2011).
These UV images show that the feathers preserved on the slab are genuinely associated with the skeleton and that their arrangement and orientation is likely correct.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com