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■ Figure 6-21 Example configuration of a dot blot (left) and a slot blot (right). The target is spotted in duplicate, side by side, on the dot blot. The last two rows of spots contain positive, sensitivity and negative control followed by a blank with no target. The top two rows of the slot blot gel on the left represent four samples spotted in duplicate, with positive, sensitivity and negative control followed by a blank with no target in the last four samples on the right. The bottom two rows represent a loading or normalization control that is often useful in expression studies to confirm that equal amounts of DNA or RNA were spotted for each test sample.

■ Figure 6-21 Example configuration of a dot blot (left) and a slot blot (right). The target is spotted in duplicate, side by side, on the dot blot. The last two rows of spots contain positive, sensitivity and negative control followed by a blank with no target. The top two rows of the slot blot gel on the left represent four samples spotted in duplicate, with positive, sensitivity and negative control followed by a blank with no target in the last four samples on the right. The bottom two rows represent a loading or normalization control that is often useful in expression studies to confirm that equal amounts of DNA or RNA were spotted for each test sample.

Genomic Array Technology

Array technology can be applied to gene (DNA) analysis by performing comparative genome hybridization and to gene expression (RNA or protein) analysis on expression arrays. There are several types of array technologies, including macroarrays, microarrays, high density oligo-nucleotide arrays, and microelectronic arrays.

Macroarrays

In contrast to Northern and Southern blots, dot (and slot) blots offer the ability to test and analyze larger numbers of samples at the same time. These methodologies are limited, however, by the area of the substrate material, nitrocellulose membranes, and the volume of hybridization solution required to provide enough probe to produce an adequate signal for interpretation. In addition, although up to several hundred test samples can be analyzed simultaneously, those samples can be tested for only one gene or gene product. A variation of this technique is the reverse dot blot, in which several different probes are immobilized on the substrate, and the test sample is labeled for hybridization with the immobilized probes. In this configuration, the terminology can be confusing. Immobilized probe is sometimes referred to as the target, and the labeled specimen DNA, RNA, or protein is called the probe. Regardless of the designation, the general idea is that a known sequence is immobilized at a known location on the blot, and the amount of sample that hybridizes to it is determined by the signal from the labeled sample.

Reverse dot blots on nitrocellulose membranes of several to several thousand targets are macroarrays. Radioactive or chemiluminescent signals are typically used to detect the hybridized targets in the sample. Macroarrays are created by spotting multiple probes onto nitrocellulose membranes. The hybridization of labeled sample material is read by eye or with a phosphorimager (a quantitative imaging device that uses storage phosphor technology instead of x-ray film). Analysis involves comparison of signal intensity from test and control samples spotted on duplicate membranes.

Although macroarrays greatly increase the capacity to assess numerous targets, this analysis system is still limited by the area of the membrane and the specimen requirements. As the target number increases, the volume of sample material required increases. This limits the utility of this method for use on small amounts of test mate-

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