Microarrays scanning

Microarray scanning ScanArray 5000 Standard Biochip Scanning System (Packard Biochip Technologies, Inc., Billerica, MA). 

Timlin, J.A., Haaland, D.M., Sinclair, M.B., Aragon, A.D., Martinez, M.J., and Werner-Washburne, M., Hyperspectral microarray scanning impact on the accuracy and reliability of gene expression data, BMC Genomics, 6, 2005. 

Lab on chip Monitoring Nanosensors Point-of-care diagnostics Protein microarrays Scanning probe microscopy... 

Another type of microchip uses bound proteins instead of DNA. These protein arrays are based on interactions between proteins and antibodies (Chapter 14). For example, antibodies to known diseases can be bound to the microarray. A sample of a patient s blood can then be put on the microarray. If the patient has a particular disease, proteins specific to that disease bind to the appropriate antibodies. Fluorescently labeled antibodies are then added and the microarray scanned. The results look similar to the DNA microarrays discussed previously. Figure 13.32 shows how this would work to identify that a patient had anthrax. This technique is growing in popularity and power, but is limited by whether purified antibodies have been created for a particular disease. 

Proceed immediately with microarray scanning (see Subheading 3.7.),... 

Fig. 5 Image of a SYBR Gold-stained Codelink microarray scanned at 532 nm, showing four replicate blocks and variation in DNA concentration within them. The blocked shde was stained with 1/2500 SYBR Gold (Molecular Probes) in 2X SSC/0.1% Triton-XlOO for 45 min at RT, and washed with 2X SSC/0.1% Triton-XlOO (twice) and 2X SSC (twice)...

MJ. Schermer, Confocal scanning microscopy in microarray detection, in DNA Microarrays A Practical Approach (M. Schena, ed.), p. 17, Oxford University Press (1999). 

An array or a matrix of nucleic acid probes immobilized at discrete locations on a silicon or glass surface provides a convenient means to simultaneously probe a sample for the presence of many different target sequences. Microarray biochip scanning devices, mostly based on fluorescent labels, are now currently available, and could also be used with CL labels to take advantage of the higher sensitivity of this detection principle. 

The steps involved in the image acquisition process for cDNA microarrays have been reviewed and a number of image analysis programs are available to mediate this process. The process can be described in four basic steps (1) scanning, (2) spot recognition, (3) segmentation (4) intensity measurement, and (5) ratio calculation (Leung and Cavalieri, 2003). 

The question is similar to asking how many times one can strip and reuse a microarray before performance deteriorates. An alternative approach is provided by Hessner et al. (2003a) in which the cDNA probes are permanently labeled using fluorescein-labeled primers to the clone s vector insert region. Fluorescein is excited at 488 nm and emits at 508 nm, while Cy3 may be excited at 543 nm to reduce any spectral overlap with fluorescein. Thus, fluorescein-labeled cDNA probes may be printed down and the slide scanned for QC/QA purposes prior to hybridization. Since the same region is primer-labeled in each cDNA, a direct comparison between the relahve fluorescence units (RFUs) and the amount of cDNA probe can be defermined. 

Figure 4.42 Examining microarray backgrounds using hyperspectral scanning. (From Martinez, M.J. et al., Nucleic Acid Res., 31(4), 1-8, 2003. With permission.)...

Timlin, JA. (2006) Scanning microarrays current methods and fiitirre directions. Methods Enzymol. 411, 79-98. 

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