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Abstract The effects of two different sample labeling methods on background signal intensities for highdensity 60mer oligonucleotide microarray were investigated. Peripheral blood samples from five disease and five control subjects were collected. Total RNA targets from peripheral blood mononuclear cells were extracted and labeled with RDPCR protocol, which were hybridized to Agilent Human 1B oligonucleotide microarrays in a twocolor comparative format. The positive control targets were labeled with the directly incorporated fluorescentlylabeled dNTP labeling. The SPSS program was performed to test normality of the dataset, variance homogeneity between the groups, coefficients of variation (CV) and analysis of variance. The results showed that the background signal intensities of Cy3 channel were higher than those of Cy5 channel. The differences of background signal intensities between the RDPCR approach and the directly incorporated fluorescentlylabeled dNTP labeling were extremely significant (PCy3<0.01, PCy5<0.01). It is concluded that the RD-PCR is a potential and useful sample labeling method with lower background signal intensities for studying highdensity long oligonucleotide microarray.
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Received: 06 February 2006
Published: 25 January 2006
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