We have previously described the relative quantitation methods.
19 For relative quantitation normalized to GAPDH, standard curves for MMPs and TIMPs and their counterpart GAPDHs were constructed with a serial dilution of total RNA of four different cell lines: HT-1080 cells (human fibrosarcoma cell line; ATCC, Manassas, VA) for MMP-1, -2, -14, -15, -16, -19, and -24; CCF-STTG1 cells (human astrocytoma; ATCC) for MMP-3, -11, and -17, CBSM cells for MMP-12, and TM endothelial cells for TIMP-1, -2, -3, -4. Using three C
T values (i.e., threshold cycle, defined as the fractional cycle number at which the amount of amplified target reaches a fixed threshold) to each input amount of dilution, standard curve equations for MMPs, TIMPs, and their counterpart GAPDHs were generated. Comparative ΔC
T method was used for relative quantitation for those genes whose absolute value of the slope of log input versus ΔC
T was less than 0.1. The relative standard curve method was used for genes not satisfying the criteria. The coefficient of variation (CV; percentage) was used for data reproducibility. Reproducibility of standard curves of GAPDHs obtained from those cell lines used for different genes was as follows: 4.45 to 5.57 of CV (percentage) for HT-1080, 2.27 to 3.61 of CV for CCF-STTG1, and 0.98 to 2.38 of CV for cultured TM cells. All triplicates of C
T used for the experiment showed much less than 1% CV. According to the manufacturer’s protocol, triplicates showing less than 2% CV are acceptable for this assay (ABI).