Total RNA extracted from conjunctival fibroblasts was used to determine the relative induction of m-CSF, type I collagen, and HSP47 in IL-4–treated fibroblasts, by real-time PCR, as described in earlier studies.
17 28 33 34 The primers and probe used for detecting mRNA for m-CSF, type I collagen, and HSP47 are as follows: m-CSF, forward TGC AGC GGC TGA TTG ACA, reverse TTC AAC TGT TCC TGG TCT ACA AAC TC, probe (
TaqMan; Applied Biosystems, Foster City, CA) FAM-TCA GAT GGA GAC CTC GTG CCA AAT TAC ATT-TAMRA; type I collagen: forward CCT CAA GGG CTC CAA CGA G, reverse TCA ATC ACT GTC TTG CCC CA, probe (
TaqMan) FAM-ATG GCT GCA CGA GTC ACA CCG GA-TAMRA; HSP47: forward CGC CAT GTT CTT CAA GCC A, reverse CAT GAA GCC ACG GTT GTC C, probe (
TaqMan) FAM-CTG GGA TGA GAA ATT CCA CCA CAA GAT GG-TAMRA. Each PCR reaction contained equivalent amounts of total RNA. Real-time PCR was performed in duplicate with a kit according to the manufacturer’s recommendation (
TaqMan; One-step RT-PCR master mix reagents kit; Applied Biosystems). All the reactions were controlled by standards (nontemplate control and standard positive control). When extracting the total RNA from conjunctival fibroblasts, we have routinely used DNase to prevent DNA contamination. Moreover, when real-time PCR was performed without adding reverse transcriptase, no PCR product was detected for the m-CSF, type I collagen, HSP47, or housekeeping genes. The quantity of mRNA was calculated by normalizing the
C T (threshold cycle) of m-CSF, type I collagen, or HSP47 to the
C T of the housekeeping genes 18S ribosomal RNA or glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of the same RNA probe, according to the following formula: the average 18S or GAPDH
C T (each multiplex PCR was performed in duplicate) was subtracted from the average m-CSF, type I collagen, or HSP47
C T, with the result representing Δ
C T. This Δ
C T is specific and can be compared with the Δ
C T of a calibration sample (for example, control conjunctival fibroblasts). The subtraction of control Δ
C T from the Δ
C T of OCP fibroblasts is referred as ΔΔ
C T. The relative quantification of expression of m-CSF, type I collagen, or HSP47 (in comparison with the control) was determined by using the value of 2
− ΔΔC T . For all the probes, the quencher dye was 6-carboxy-tetramethyrhodamine (TAMRA), and the reporter dyes were 6-carboxy-fluorescein (FAM) for m-CSF, type I collagen, and HSP47, and VIC for 18S or GAPDH.