Retinas of three to five animals per age group were isolated through a cut in the cornea, snap-frozen separately in liquid nitrogen, and stored at −80°C until further processing. The following ages were examined (the number of specimen per age appears in parentheses): rd1 mice at P7 (4), 11 (4), 14 (5), 21 (4), 28 (5), 60 (4), 120 (3) (total n = 29); rds mice at P7 (3), 14 (3), 17 (3), 21 (4), 28 (3), 60 (3), 120 (4), 280 (4) (total n = 27); wt mice at P7 (4), 11 (4), 14 (4), 17 (3), 21 (4), 28 (4), 60 (5), 120 (4), 280 (3) (total n = 35); RCS rats at P8 (3), 15 (3), 22 (4) 28 (4), 35 (4), 43 (4), 60 (4) (total n = 26); and SD rats at P8 (3), 15 (3), 22 (4), 28 (4), 35 (3), 43 (3), 60 (3) (total n = 23).
After homogenization of the retinas, RNA was isolated (RNeasy MiniKit; Qiagen, Hilden, Germany), including a DNase treatment step to remove any contamination of genomic DNA, according to the manufacturer's instructions (RNase-Free DNase Set; Qiagen). RNA concentration was spectrophotometrically measured and its purity confirmed with 260-nm/280-nm absorbance ratios. RNA was reverse transcribed with a kit (QuantiTect Reverse Transcription Kit; Qiagen).
Equal amounts of cDNA were applied for PCR amplification in triplicate in a thermocycler (LightCycler; Roche, Mannheim, Germany), using SYBR green master-mix (SYBR Green JumpStart
Taq ReadyMix for qPCR Capillary Formulation; Sigma-Aldrich, Stockholm, Sweden) with a total reaction volume of 10 μL in each glass capillary (LightCycler Capillaries; Roche). The primers indicated in
Table 1 were used in a final concentration of 0.25 μM. PCR conditions were set to 95°C for 10 minutes' initialization, followed by 45 cycles of 5 seconds' denaturation at 95°C, 8 seconds' annealing at 62°C, and 4 to 12 seconds' elongation at 72°C. Fluorescence from the SYBR green that binds to double-stranded DNA was measured at the end of each extension period. A calibrator sample, produced by mixing samples of different genotypes and ages from either mouse or rat tissue, provided a constant calibration point for all samples within and between runs. A software program (LightCycler Relative Quantification Software, ver. 1.01; Roche) automatically calculated ratios between calibrator-normalized target and reference. To verify the absence of genomic DNA contamination, control samples were run in which no reverse transcriptase was included. Also, controls without cDNA but only water were included in some experiments. Specificity of the PCR template was verified by melting-curve analysis. Subsequent gel electrophoresis assured amplification of only one PCR product of the expected size. A spreadsheet (Excel; Microsoft, Redmond, WA) was used for further data analysis and graphical visualization. Statistical evaluation was performed online (two-sample
t-tests,
F-test, one-way ANOVA, Tukey's HSD procedure for independent samples,
http://faculty.vassar.edu/lowry/VassarStats.html).