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Background hybridization and probe saturation interfere with low-level and high-level detection.
Today, the sensitivity, dynamic range, and resolution of DNA microarrays are limited by interference, noise, probe saturation, and other sources of errors in the analyte detection procedure.
Especially in organs with the highest accumulation of the fluorescent probe, saturation of the fluorescent signal can occur, which will, without the dilution approach, result in an underestimation of the signal in the particular organ (Figure 2b).
PMT voltage settings were varied to obtain maximum signal intensities with <5% probe saturation.
Otherwise the probe saturation concentration or the approximate probe concentration can be deduced by a simple target concentration titration experiment.
To some extent the small changes reflect the fact that the hybridization isotherms for oligonucleotide arrays are frequently not linear due to probe saturation [11].
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Moreover, the observed lower sensitivity of the SNV detection in samples with higher CN may reflect capture-probe saturation and indicates the need for adjustment of sequencing depth and CN.
Our expectation was that if the Turtle Probes were converted to closed circles with a higher efficiency than the corresponding Padlock Probes, the same number of signals should be obtained with less probe (less saturation of targets).
The remaining reference RNAs are added in increasing concentrations Lys < Phe < Thr < Dap with Dap being the highest and close to the probe signal intensity saturation level.
After normalization, probes exhibiting saturation or signals that were not above background were removed (10 and 82 probes, respectively), leaving 21801 probes for examination of expression patterns.
The probe intensity measured in the microarray experiment is given to a good approximation by the hyperbolic function [ 18, 19, 24- 27] (3) I p P = Mx X p P,S × w p P,S + X p P,N × w p P,N 1 + X p P,S + X p P,N + O with p ≡ g,k where M is the maximum intensity upon complete saturation of the probes and O is the optical background.
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