Microarray signal intensities

Quantification of the Microarray Signal Intensities and Qnality Control. . 77... 

To overcome photobleaching and the low signal intensities of cyanine dyes Cy3 and Cy5, these dyes were encapsulated in silica coreshell nanoparticles [76]. The obtained dye-doped nanoparticles were applied in the DNA microarray-based... 

Fig. 5. Measurement of the relative amount of protein immobilized in each spot in the array. A p53 protein function microarray probed with a Cy3-labeled anti-His antibody. Quantification of the signal intensity from each spot reveals the relative amounts of recombinant protein present in each spot in the array.

Figure 8 Boxplots of normalized intensity values across arrays, boxplots facilitate comparison of sample distributions and dynamic range across microarrays. If the microarrays follow different data distributions increased false positive and negative rates may be demonstrated. The depicted signal is the log2 of the normalized feature signal intensity.

Data obtained from microarray detection instruments are expressed in units of fluorescent counts with 16-bit values ranging from 1 to 65 536. It is conunon practice to convert or transform the raw counts into a logarithmic scale. Microarray data transformed into a log scale (0-. 8) exhibit a more uniform distribution than raw signal intensities (1-65536). 

The basis of contemporary microarray technology is printing known oligonucleotide sequences in predefined positions onto the array surface, which then capture the labeled complementary strands from the sample, following the complementarity rules (duplex forming and hybridization). After hybridization, the original amount of mRNA molecules can be estimated from the signal intensity of the captured/hybridized molecules. In the case of the microscope slide-based microarrays (also referred to as cDNA microarray), presynthesized complementary DNA molecules are attached to a solid surface [40]. 

This report shows how a working prototype for nucroarray hybridizations based on the shear-driven technology has been developed and tested. The key factor for the success of the SDH method was the combination of the mixing, circumvented the slow molecular diffusion, and the reduction of sample volume generated more concentrated samples and higher final intensity values of the microarray spots. The concentration was indeed found to be a major factor on the effect of convection to reach higher signal intensities. 

Microarrays are used for detection and quantification of the target gene using a DNA chip on which known DNA molecules are fixed. Complementary DNAs (cDNA) are reverse transcribed from RNAs isolated from culture samples, and the DNA extracted from environmental samples is hybridised to the nucleotide probes on the DNA chip. The signal intensities of these DNA-probe hybridised molecules are then detected using a fluorescence scanner. 

Data analysis is a critical part of lectin microarray experiments, because the data obtained from each microarray analysis shows systematic variation in microarray quality, scanner detection stability, sample preparation reproducibility, and labeling efficiency. For this purpose, an initial step to normalize the obtained signal intensities is essential. In this section, the two fundamental procedures required for data analysis are described [42 4]. 

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