After PCR, a thermal melt profile was performed to examine the homogeneity of the PCR application. Each DNA sam ple was analyzed in duplicate, and the mean quantity was used for further analysis. Relative quantification of the amplified gene levels in the bisulfite converted genomic DNA sample was performed by measuring the threshold cycle values of target genes and B actin. The mean quantity of genes was divided by the mean quantity of ACTB and was used for the normalization of input DNA. The negative values for ACTB were excluded from the methylation analysis. The bisulfite converted genomic DNA of a known concentration was drawn at 1, 1 4, 1 16, and 1 64 via serial dilutions, and then used in a standard curve for quantification. The modified genomic DNA by CpG methyltransferase M.

SssI was used as a positive control according to the manufac turers recommendations. DNA methylation according to M. SssI was verified using the restriction enzyme BstUI. Reverse transcription PCR mRNA was extracted using the commercial RNeasy SB-480848 chemical structure Mini kit according to the manufacturers recommendations. The mRNA was eluted in 20 uL of DEPC water and quantified with a NanoDrop ND 100 device. One microgram of mRNA from each sample was sub jected to cDNA synthesis using Maloney murine leukemia virus RT and random hexamers. cDNA synthesis was performed according to the manufacturers recommendations by mixing 1 uL of 1 ug mRNA, 4 uL 5X RT buffer, 1 uL 500 nM oligo dT, 1 uL 10 mM dNTP, 0. 5 uL RNasein, 1 uL M MLV reverse tran scriptase, and 11. 5 uL dH2O in PCR tubes. The mixture was then incubated at 37 C for 1 h.

cDNA was diluted with 20 uL dH2O and stored at 80 C until use. Primers were designed using primer3 version 0. 4. 0 and are shown in Additional file 1, Table S2. cDNA was amplified by PCR with primers for each target gene. The RT PCR program was as follows, 95 C for 10 min, followed ESI-09 ic50 by 35 cycles at 95 C for 15 s, 60 C for 15 s, and then at 72 C for 45 s. ACTB was amplified simultaneously with the other PCR products and was used as a control for RNA integrity. Chemical treatment To determine the optimal concentration of 5 aza 2 deoxycytidine and vincristine in CRC cell lines, we measured cell viability with the MTT assay according to the manufacturers recommendations using MTT reagents and dimethyl sulfoxide. To iden tify the demethylating effect of treatment with anticancer drugs, CCD18Co, SW480, DLD 1, and LoVo cells were seeded in six well culture plates at a density of 0. 5 × 105 cells per well. After 24 h, cells were cultured in serum free media con taining either 30 uM 5 aza dC or 100 nM vincristine in 10 uL dimethyl sulfoxide for 48 h at 37 C in a 5% CO2 at mosphere. After 48 h, cells were washed in PBS three times and then harvested.