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When choosing a small minimum inter-probe distance (≪probe-length) for the intergenic regions a "selective tiling" is achieved, i.e. high density, but with high quality probes only (see Table S1 for maximum probe density).
To achieve maximum probe density using a minimum number of probes, the following probe selection strategy was used: first, all 25 basepair fragments were sequentially extracted from the set of 235 sequences.
In addition, we used the degree of skewness (S) of the PCC distributions as a means of identifying histone marks with maximum probe density showing positive correlation with RNAPII occupancy.
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Under the proposed experiment condition, 0.1 μg/ μL of IPC (green dotted line in Figure 2(a)) could be considered as an optimal probe density for the maximum target hybridization rate and its signal response.
The proposed MEMS probe card configuration potentially improves the probe density and simplifies the fabrication process.
As microarray probe density continues to increase, a 2% probe failure rate represents a substantial cost in data loss.
High probe density results in each of the transcription units being represented by multiple probes, in contrast to "one-probe-one-gene" in expression microarrays.
This probe density trade-off is balanced between the feature number and the biological questions asked.
The probe density parameter details can be found in Table S1.
Probe density of probe sets used in this study.
This selectively omits or reduces the probe density in SDs.
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Justyna Jupowicz-Kozak
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