To obtain adequate amounts of mRNA, we grew ∼250,000 cells in 6-cm dishes on surfaces that measure 2.8 × 3.0 cm. For each data point, cells from two or three surfaces were pooled. The mRNA was extracted from the cells after they had been grown on either planar or 400-nm pitch surfaces for 4 days. This period was used so that parallel cultures, either untreated or treated with 10
−7 M dexamethasone, could be harvested to assess any possible interaction of dexamethasone and topographic cueing on myocilin expression. The mRNA was extracted with RNeasy kits according to the manufacturer’s protocol (Qiagen, Valencia, CA). The amount of mRNA was measured, and 75 ng was used with the one-step kit for real-time PCR (
TaqMan; Applied Biosystems, Inc., [ABI] Foster City, CA). Individual reactions with the real-time PCR machine (StepOne; ABI) were performed with a total volume of 10 μL. The reverse transcription reaction was performed for 20 minutes at 50°C followed by PCR enzyme activation for 10 minutes at 95°C. Forty cycles of 60°C for 1 minute followed by 95°C for 15 seconds were performed. The reference mRNA was the 18S ribosomal RNA. At least three reactions were run for each sample. The mean ± SD was determined for each reaction and a Student’s
t-test was used to determine statistical significance. To assess the levels of mRNA of the versican isoforms, 1 μm of mRNA from the cells was reverse transcribed into cDNA (Retroscript kit; Ambion, Austin, TX), according to the protocol supplied. The relative levels of each of the versican isoforms were determined (Power SYBR green PCR Master Mix kit; ABI) with 75 ng of cDNA and primers that had been reported previously to be characteristic of each of the isoforms.
23 The PCR cycles were the same as the myocilin reactions. The samples were performed in triplicate and then normalized to the V0 isoform from the control planar sample. The planar V0 isoform was assigned a value of 1.0. The 18S ribosomal DNA was the reference DNA for these samples. The mean ± SD was determined for each reaction, and a Student’s
t-test was used to determine statistical significance. The difference (
n-fold) between the planar value and the value on the 400-nm pitch surfaces for each condition was also determined by dividing the mRNA from the 400-nm pitch surface by the planar value.