Total RNA was extracted from RPE cells using a kit (RNeasy; Qiagen, Inc.) and treated with DNase (Qiagen, Inc.) while on the column according to the manufacturer’s protocol. The RNA’s quality and integrity were checked as just described, and the RNA was used to make cDNA. The 20-μL reverse transcription reaction consisted of 1× buffer (Omniscript; Qiagen, Inc.), 0.5 mM of each dNTP, 10 U RNasin (Promega, Madison, WI), 4 U reverse transcriptase, 1 μg total RNA, and either 500 ng oligo (dT)
15 primer (Promega; if PGES mRNA was to be measured) or 50 ng random hexamer primer (Promega; if COX-2 mRNA was to be measured). The reaction mix was covered with approximately 0.1 mL of mineral oil (Molecular Biology Grade, Sigma-Aldrich, St. Louis, MO), incubated at 37°C for 1 hour, diluted to 150 μL with water, and incubated in a boiling water bath for 10 minutes. Real-time PCR reactions were performed with a core reagent kit (SYBR Green PCR; Applied Biosystems, Foster City, CA). Messenger RNA levels for ribosomal protein, large, P0 (RPLP0) were measured as an internal standard.
16 17 Five microliters of the appropriate diluted reverse transcription mix (heated for 3 minutes in a boiling-water bath and quenched in ice water immediately before use) were added to a 96-well plate followed by 45 μL of PCR master mix. The final volume of the PCR reaction was 50 μL and consisted of 1× buffer (SYBR Green I; Applied Biosystems), 3 mM MgCl
2, 1 mM dNTP (0.2 mM each dNTP and 0.4 mM dUTP), 0.1 μM each of the appropriate forward primers (COX-2: 5′-GCC TGA TGA TTG CCC GAC T; mPGES: 5′-ACA TCT CAG GTC ACG GGT CTA; RPLP0: 5′-TTA AAC CCC CTC GTG GCA ATC) and reverse primer (COX-2: 5′-GCT GGC CCT CGC TTA TGA TCT, mPGES: 5′-TTC CTG GGC TTC GTC TAC TC; RPLP0: 5′-CCA CAT TCC CCC GGA TAT GA) and 1.25 U of
Taq polymerase (Ampli
Taq Gold; Applied Biosystems). The RPLP0 primers work with cDNA primed with oligo(dT)
15 or random hexamers. The concentration of RPLP0 cDNA was measured for all cDNAs at the same time the concentration of cDNA for the gene of interest was determined. The PCR products were detected with a real-time detection system (iCycler IQ; Bio-Rad Laboratories, Hercules, CA). Primers were designed using a computer program (Oligo; Molecular Biology Insights Inc., Cascade, CO) to cross an exon–exon boundary to minimize the chance that a signal was from contaminating DNA. To check that genomic DNA was not a problem, real-time PCR was performed, using mock reverse-transcription reactions in which the reverse transcriptase was omitted. All real-time PCR reactions included a melt curve to examine the specificity of PCR product and to ensure that primer-dimer artifacts did not interfere with the measurements. The real-time PCR assays were performed in triplicate for each sample, and the average cycle at which the PCR product crossed the threshold (Ct) was calculated. The ratio of target gene mRNA expression relative to that of the internal standard mRNA (RPLP0) was calculated according to the method of Pfaffl
18 (see the following equation, where E is the efficiency of real-time PCR amplification for the appropriate gene).
\[\mathrm{ratio}\ {=}\ \frac{(\mathrm{E}_{\mathrm{target}})^{{\Delta}\mathrm{Ct}_{\mathrm{target\ (control-treated)}}}}{(\mathrm{E}_{\mathrm{RPLP0}})^{{\Delta}\mathrm{Ct}_{\mathrm{RPLP0\ (control-treated)}}}}\]