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The membranes were hybridized with this cDNA probe labeled with [α-32P]deoxy-CTP by the random hexamer method as in Roy et al.[93].[93]
The latter identifies false variants introduced by the random hexamer priming during the library construction.
Many of these are ultimately converted to double stranded DNA by the random hexamer primers.
TheP-labeled Umodl1 probe was synthesized from the purified coding region of mouse Umodl1 by the random hexamer labeling method.
Spelt1, Spelt52, pSc119.2, and pAs1 probes were labeled by the random hexamer method with α-P-dATP (Amersham Pharmacia Biotech, United Kingdom) using Klenow fragment [ 58].
The colonies were then transferred to a Hybond N+ membrane [ 53] and hybridized with the probe labeled by the random hexamer method using α-P-dATP (Amersham Pharmacia Biotech, UK) and a Klenow fragment [ 54].
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Our data is in agreement with their conclusion and suggests that a majority of the bias is likely due to priming by the random hexamers and the preference of the DNA polymerase for certain primer:template junctions.
The reaction was stopped at 70°C for 10 mins followed by pooling of the random hexamer and oligo dT) reactions of the same sample.
As the CG content of UTRs (20%) was notably lower than the CG content of the ORFs (43%), a systematic bias against AT rich sequences may have been introduced by less efficient annealing of the random hexamer primers during first strand cDNA synthesis.
MDA could produce these in a three step process; 1) initial extension of the random hexamer primers by strand displacement synthesis in which the phi29 DNA polymerase displaces 5'-ends, 2) displacement of extended 3'-ends by branch migration, and 3) mispriming of the 3'-ends on the nearby displaced 5'-strands.
Interestingly, the degree of coverage varied across the genome, though the shape of coverage distribution curves was similar for both samples (Figure 3), indicating that some bias may have been introduced by the use of random hexamer primers and the mapping process to result in different extents of very deep coverage.
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