To compare transcription levels of a panel of genes in the differently treated HCE cells, real-time RT-PCR was performed. Thus, HCE cells were grown for 14 days with 10% FBS or 20% AS, PRP, and PRGF, in the presence or absence of supplements. Total RNA was extracted according to the manufacturer's protocol (RNeasy minikit; Qiagen Inc., Valencia, CA), and treated with DNase for 30 minutes at 37°C and 10 minutes at 65°C (Promega, Madison, WI). Total RNA was quantified, tested on an agarose gel, and stored at −80°C until use.
For each sample, cDNA was synthesized from 0.5 μg total RNA using the iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA). Real-time PCR assays were performed with an iCycler PCR platform (Bio-Rad). The reaction mixture contained 1 μL cDNA from the RT reaction, together with forward and reverse specific primers (250 nM each) and iQSYBR Green Supermix (Bio-Rad) in a final reaction volume of 20 μl. Thermal cycling conditions were as follows: An initial polymerase activating step at 95°C for 3 minutes, followed by 60 cycles for 20–30 seconds each at 95°C (denaturation step), 20–30 seconds at the corresponding annealing temperature for each gene (
Table 1), and 20–30 seconds at 72°C (extension step), during which data were collected. Each assay included a negative control consisting of the absence of cDNA. Expression data were generated from 4 amplification reactions with samples and controls run in triplicate, and performed on different cDNA samples reverse transcribed from RNA prepared from independent culture assays. Optical data obtained by real-time PCR were analyzed using the MyiQ Single-Color Real-Time PCR Detection System Software, Version 1.0 (Bio-Rad). The dynamic range of detection for each gene was determined by preparing 5-fold serial dilutions of control HCE cells (undiluted, 1:5, 1:25, 1:125, and 1:625). The reliability of real-time PCR was defined by regression analysis of average Ct versus the log
10 of the target copy number. PCR efficiency was around 93% with all primer pairs. Melt Curve analysis of each PCR assay and 1.5% agarose gel electrophoresis analysis of randomly selected samples were performed to confirm the specificity of the amplification products. The expression of three different housekeeping genes (
GAPDH, β-actin, and
RIG/S15) also was analyzed. They were chosen after verifying their suitability by geNorm software (version 3.5). They were used to normalize expression data obtained from the studied genes, using the Bio-Rad Gene Expression Macro Software Version 1.1 derived from the algorithms outlined by Vandesompele et al.
31 All primers were synthesized commercially (Isogen Life Sciences, Barcelona, Spain) and a BLAST search was performed to verify their specificity for their target DNA sequences. The sequences of the primer pairs, as well as the size of the corresponding amplified fragments are detailed in
Table 1.