Systematic Screening of Gene Expression Using a cDNA Macroarray - Drugs of Abuse: Neurological Reviews and Protocols - page 242

1.2.1. Macroarray
Macroarrays are generally defi ned by the deposition of probes deposited onto
membranes or plastic and by the use of radioactivity for detection. The term
macroarray, as opposed to microarray (discussed next), also refers to the lower
probe density on these arrays. Although density varies among arrays, the term
macroarray is useful because of other inherent differences of membrane-based
arrays. Currently, DNA clones, PCR amplicons, or oligonucleotides are spotted
onto membranes using spotting robots or ink-jet-like printers. Macroarrays are
unique among hybridization arrays in that they generally use radioactive target
labeling. After the target is radioactively labeled, control and experimental
samples are hybridized to individual and separate arrays. Phosphorimagers
(or less frequently X-ray fi lm) are then used to detect the bound target. These
arrays, typically containing between 200 and 8000 genes, are commercially
available for a wide variety of organisms and genes and can be obtained from a
number of companies. “Custom” macroarrays can also be constructed in-house
and may contain as few as a dozen or as many as thousands of genes. The
experimental protocols described in this chapter are conducted exclusively with
membrane-based macroarrays obtained from Clontech (www.clontech.com).
1.2.2. Microarray
Microarrays can be differentiated from macroarrays in three ways. First,
microarrays generally use silicon/glass as a matrix and, second, they use
fl uorescent dye-labeling detection. Microarrays also tend to have a larger
number and higher density of probes than macroarrays. As with macroarrays,
probes are made from clones, PCR amplicons, or oligonucleotides spotted
robotically onto the matrix surface. This approach has advantages in that
hybridization takes place in a fl ow cell or small hybridization chamber, which
uses a much smaller hybridization solution volume as compared to macroar-
rays, thereby increasing the relative target concentration and decreasing costs.
Moreover, a competitive fl uorescent scheme allows both sample groups (control
and treated) to be hybridized to the same array using distinct fl uorescent
dyes (typically Cy3 and Cy5). Like macroarrays, an ever-expanding number
of microarrays are commercially available. Many research institutions are
currently investing heavily in the equipment to produce custom microarrays
in-house.
1.2.3. High-Density Oligonucleotide Arrays (Affymetrix)
High-density oligonucleotide arrays differ from other formats in that the
probe is generated in situ on the surface of the matrix. The leader in this
type of array is Affymetrix (Santa Clara, CA), a company that uses a unique