TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><strong>Background</strong>: Aberrant DNA methylation occurs frequently in cancer. The aim of this study was to identify novel methylation markers in lung cancer in Xuanwei, China, through integrated genome-wide DNA methylation and gene expression studies.</p>
<p><strong>Methods</strong>: Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected on 10 paired lung cancer tissues and noncancerous lung tissues by methylated DNA immunoprecipitation combined with microarray (MeDIP-chip) and gene expression microarray analyses, respectively. Integrated analysis of DMRs and DEGs was performed to screen out candidate methylation-related genes. Both methylation and expression changes of the candidate genes were further validated and analyzed.</p>
<p><strong>Results</strong>: Compared with normal lung tissues, lung cancer tissues expressed a total of 6,899 DMRs, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Integrated analysis of DMRs and DEGs identified 45 tumor-specific candidate genes: 38 genes whose DMRs were hypermethylated and expression was downregulated, and 7 genes whose DMRs were hypomethylated and expression was upregulated. The methylation and expression validation results identified 4 candidate genes (<em>STXBP6</em>, <em>BCL6B</em>, <em>FZD10</em>, and <em>HSPB6</em>) that were significantly hypermethylated and downregulated in most of the tumor tissues compared with the noncancerous lung tissues.</p>
<p><strong>Conclusions</strong>: This integrated analysis of genome-wide DNA methylation and gene expression in lung cancer in Xuanwei revealed several genes regulated by promoter methylation that have not been described in lung cancer before. These results provide new insight into the carcinogenesis of lung cancer in Xuanwei and represent promising new diagnostic and therapeutic targets.</p>

[BEFORE_START]
<p><span style="font-size: small;">Cy dyes are light sensitive. Be sure to minimize light exposure of the dyes during use and<br />store in the dark when not in use.<br /><span style="color: #006fba;"> </span></span><span style="font-size: small;">Cy dyes are ozone sensitive. Take the necessary precautions to keep atmospheric ozone<br />levels below 20 ppb (parts per billion).<br /><span style="color: #006fba;"> </span></span><span style="font-size: small;">Cy dyes are humidity sensitive. Take the necessary precautions to keep humidity levels<br />below 40%.<br /><span style="color: #006fba;"> </span></span><span style="font-size: small;">Roche NimbleGen has found that using VWR water and DTT for all post-hybridization<br />washes results in higher signal from Cy dyes.</span></p>
<p><span style="font-size: small;">Roche NimbleGen recommends using a NanoDrop Spectrophotometer for quantifying<br />and characterizing nucleic acid samples because this instrument requires only 1.5 μl of<br />sample for analysis.<br /><span style="color: #006fba;"> </span>Perform all centrifugations at +15 to +25°C unless indicated otherwise.</span> </p>

[GUIDELINES]
<p><span style="font-size: small;">The first part of the process requires quality control of experimental (IP) and control (input)<br />samples to verify quality prior to microarray hybridization. You then independently label<br />these samples using a NimbleGen Dual-Color DNA Labeling Kit and co-hybridize them to a<br />NimbleGen DNA Methylation array using a NimbleGen Hybridization System. Following<br />hybridization, the arrays are washed, dried, and scanned using a NimbleGen MS 200<br />Microarray Scanner. Array data are extracted and analyzed using our NimbleScan software<br />and SignalMap software.</span></p>
<p><span style="font-size: small;">Then various verification experiments were carried out.</span></p>

[STEPS]
SECTION: MeDIP-chip
?. 
SECTION: Gene expression microarray
?. 
SECTION: Methylation-sensitive high-resolution melting assay (MS-HRM)
?. 
SECTION: Sequenom MassARRAY platform
?. 
SECTION: Real-time fluorescent quantitative PCR
?. 
SECTION: Western blotting
?.