cDNA

cDNA clones are PCR amplified and the PCR products are printed on to slides with micropins. The clones are verified by sequencing.

cDNA array is hybridized with Cy-dye labeled sample and identical control for the same set of experiments.

Data from different sets of experiments are difficult to compare because different controls are used.

Although frequently called cDNA array, genomic DNA can also be PCR amplified and printed to produce genomic DNA arrays.

Affymetrix

Affymetrix chips are oligos synthesized on the chip. The synthesis process (lithographic process) is controlled by a set of maskers.

A unique aspect of Affymetrix chip is its use of multiple "match" and "mismatch" oligos for each gene (feature).

Affy array is hybridized with labeled sample only.

Spotted oligos

Synthetic oligos may be printed using a similar process for cDNA array printing. Compared to Affy arrays, it is flexible and longer oligos may be used.

Spotted oligo array is frequently hybridized with a mix of sample and control.

Inkjet oligos

Synthetic oligos printed using the inkjet printer technology.

Membrane

cDNA spotted on hybridization filters. Flexible and economic for a small set of genes.

Radio-labeled sample is hybridized to the membrane.