Mice were killed 90 minutes after allergen challenge, and the conjunctival tissues were collected. Total RNA was isolated from the tissue samples using RNA reagent (STAT-60; Tel Test, Friendswood, TX) and purified with a purification kit according to the manufacturer’s protocol (RNeasy Mini Kit; Qiagen, Hilden, Germany). Total RNA was reverse transcribed and amplified using an aRNA kit (Amino Allyl MessageAmp; Ambion, Austin, TX) for Cy5 and Cy3 dye labeling. Cy5 dye was used to generate the experimental cRNA probe from the allergen-challenged conjunctiva, and Cy3 dye was used to generate the reference cRNA probe from the control conjunctiva. Labeled cRNA probes were hybridized on oligo-microarrays (AceGene; Hitachi, Yokohama, Japan) corresponding to 29,568 genes and were scanned (FLA-8000; Fuji Film, Tokyo, Japan). The intensities of the fluorescent signals were quantified with an array program (DNASIS Array; Hitachi). After subtraction of the background levels, the signal from the gene spots was adjusted to compensate for excitation differences between the two dyes. Then the fluorescent signal was corrected for image intensity, background/spatial artifacts, and chip-to-chip comparisons using a custom database constructed by the array program (DNASIS Array; Hitachi).