Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere. Labeled DNA from the enriched and the input pools was combined (1–2 μg) and hybridized to a NimbleGen HG18 CpG promoter Array (Roche Diagnostics GmbH, Mannheim, Germany), which contained MK 1775 all well-characterized RefSeq promoter regions [from −800 bp to +200 bp transcription start sites
(TSSs)]. Array was then washed and scanned with Axon GenePix 4000B microarray scanner. After normalization, raw data was input into SignalMap software (Roche Diagnostics GmbH, Mannheim, Germany) to observe and evaluate the methylation peaks. A customized peak-finding algorithm provided by NimbleGen was applied to analyze methylation data from MeDIP-microarray as previously described. SN-38 manufacturer The algorithm was used to perform the modified Kolmogorov-Smirnov test on several adjacent probes using sliding windows to predict enriched regions across the array. MeDIP-quantitative PCR assay A MeDIP assay, combined with qPCR, was used to evaluate quantitatively the methylation TPX-0005 supplier status of candidate genes in the tumors derived from the control and 125I treatment groups. MeDIP was performed as described above. Purified DNA from the
immunoprecipitated DNA complexes and from input DNA was analyzed by qRT-PCR on an Applied Pregnenolone Biosystems 7900 Real- Time PCR System. The experiment was performed in triplicate. The relative changes in the extent of gene methylation were determined by measuring the amount of detected genes in immunoprecipitated DNA after normalization to the
input DNA. The primer sequences are listed in Additional file 1: Table S1. Statistical analysis The results of the animal experiments and real-time PCR were analyzed using SPSS 13.0 software. (SPSS Inc., Chicago, IL, USA) All data were plotted as mean ± standard deviation. Student’s t-test was used to compare values between two independent groups. Differences were considered to be significance when p < 0.05. Results Inhibitory effect of I125 seed irradiation on the growth of gastric cancer The effectiveness of 125I seed irradiation to inhibit the growth of implanted NCI-N87 tumors was examined in nude mouse model. There were no significant changes in the tumor volumes for the first 10 days of the 125I seed treatment. However, after 13 days, the 125I-irradiated tumors were much smaller, and significant differences in tumor volumes were observed over time between the control and 125I treatment groups Figure 1A). At day 28, the mice were sacrificed and tumor weights were measured. Statistical difference in the tumor weight was observed between the control and treatment groups Figure 1B).