Mouse corneas were treated as described, removed, and stored in preservative (RNA Later; Ambion, Inc., Austin, TX) at 4°C. Total RNA was extracted from RNA (TRIzol Extraction Reagent; Gibco BRL, Grand Island, NY) according to the manufacturer’s instructions. Briefly, three corneas were pooled and 1 mL extraction reagent added at room temperature. Corneas were homogenized in three 15-second bursts with a plastic pestle (GenoTechnology Inc.) attached to a handheld drill, and the lysate was allowed to sit at room temperature for 10 minutes to allow nucleoprotein dissociation. The lysate was loaded into a shredder (Qiashredder; Qiagen, Inc., Valencia, CA) to aid homogenization, followed by centrifugation at 12,000g for 5 minutes. The supernatant was removed to an RNase-free Eppendorf tube, 200 μL of chloroform added, and the mixture vortexed. After incubation at room temperature for 10 minutes, phase separation was performed by centrifugation at 12,000g for 15 minutes at 4°C. The upper aqueous phase containing the RNA was carefully removed to an RNase-free tube and RNA precipitated by the addition of 500 μL isopropanol for 15 minutes at room temperature, followed by centrifugation at 12,000g at 4°C. The RNA pellet was washed with 75% ethanol and resuspended in 25 μL of diethyl pyrocarbonate (DEPC) water.
Reverse transcription was performed on 2 μg total corneal RNA with a kit (Superscript II Reverse Transcriptase cDNA Synthesis; Gibco BRL), according to the manufacturer’s instructions, on a commercial PCR system (GeneAmp PCR System 9700; PE-Applied Biosystems, Foster City, CA). The cDNA was diluted fivefold before PCR amplification.
Real-time PCR analysis was performed with the fluorogenic probe-based 5′ exonuclease assay (
Taqman; PE-Applied Biosystems) on an automated sequence detection system (model 7700; PD-Applied Biosystems), according to the manufacturer’s instructions. Reactions were performed in a 50-μL volume of master mix from the kit (
Taqman Universal PCR Master mix; PE-Applied Biosystems). The manufacturer’s quantitative (q)RT-PCR methodology was used to measure corneal cytokine or the adhesion molecule gene copy number, which was normalized to the ribosomal protein L32 (RPL 32) mRNA copy number.
9 Linear standard curves were created for each amplification, with 10
2 to 10
8 copies of IL-1 RA, VCAM-1, ICAM-1, or RPL32 plasmids (provided by one of the authors [IC]). Control amplification (no probe and no template) samples were included in each reaction to set baselines. All quantitation of corneal gene expression was within the linear range of amplification.