Rat eyes were enucleated immediately after death into chilled diethylpyrocarbonate (DEPC)–treated normal saline, and the retinas were dissected, snap-frozen in liquid nitrogen, and stored at –80°C. Total RNA was isolated using an RNeasy mini-kit (Qiagen, Valencia, CA). Contaminating genomic DNA was removed with DNaseI (DNA-free; Ambion, Austin, TX). Samples free of visible DNA contamination on a 1% agarose gel and with a ratio of 28S:18S rRNA approximating 2:1 were quantified by spectrophotometry. One-microgram samples with a 260:280 nm absorbance ratio of ≥1.9 were reverse transcribed using a first-strand cDNA synthesis kit (SuperScript III First-Strand Synthesis System; Invitrogen, Carlsbad, CA). A reverse transcriptase-free control sample was synthesized in parallel with each cDNA sample, with substitution of DEPC-H2O for reverse transcriptase. For purposes of normalization, a standard cDNA pool was prepared from pooled retinal RNA extracted from 10 F344, SPD, and DA rats that had been exposed to room air or cyclic hyperoxia.
Primers for rat erythropoietin (EPO) and for the housekeeping genes acidic hypoxanthine guanine phosphoribosyl transferase (
HPRT) and ribosomal phosphoprotein (
ARBP) were designed to flank an intron (Primer3 software; Whitehead Institute for Biomedical Research, Cambridge, MA)
27 and tested in silico for specificity against sequences for
Rattus norvegicus using BLAST software (NCBI, Bethesda, MD). Primer sequences were as follows: ACCAGAGAGTCTTCAGCTTCA (EPO forward), GAGGCGACATCAATTCCTTC (EPO reverse); TTGTTGGATATGCCCTTGACT (HPRT forward), CCGCTGTCTTTTAGGCTTTG (HPRT reverse); and AAAGGGTCCTGGCTTTGTCT (ARBP forward), GCAAATGCAGATGGATCG (ARBP reverse). Primers were then synthesized (Geneworks Ltd., Thebarton, SA, Australia).
Real-time RT-PCR was performed (RotorGene 2000 Thermal Cycler; Corbett Research, Mortlake, NSW, Australia). Each 20-microliter reaction mixture contained 10 μL SYBR Green master-mix (QuantiTect SYBR Green PCR Master Mix; Qiagen) containing hot-start
Taq DNA polymerase, SYBR Green I, dNTPs, and PCR buffer (5 mM MgCl
2, Tris-Cl, KCl, (NH
4)2SO
4 pH 8.7), 2 μL each forward and reverse primer (0.5 μM final concentration), and 6 μL cDNA sample diluted 1/100 with purified water (Ultra Pure; Fisher Biotech, West Perth, WA, Australia). Reaction conditions were initial denaturation (95°C, 15 minutes) followed by 50 cycles of denaturation (94°C, 20 seconds), annealing (50°C, 20 seconds), extension (72°C, 30 seconds), and final extension (72°C, 4 minutes, followed by 25°C, 5 minutes). The standard cDNA pool was included in triplicate in each PCR run, together with a single RT-negative control for each sample and two water (no-template) controls. Melt-curve analysis was used to confirm amplicon specificity. The melt-curve of each real-time PCR product was compared with that of the corresponding sequenced product.
28 Real-time RT-PCR products were separated on agarose gels, purified, sequenced, and compared with the predicted amplicon sequence to confirm identity. Purified DNA was labeled (BigDye Terminator version 3.1 Cycle Sequencing Kit; Applied Biosystems, Foster City, CA) and resolved (ABI 3100 Genetic Analyser; Applied Biosystems).