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| Status |
Public on May 03, 2013 |
| Title |
DNA methylation and expression profiling study for bladder cancer [gene expression] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.
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| Overall design |
For the integrated analysis of global methylation status and gene expression levels, we used the genome-wide human-6 v2.0 expression beadchip (Illumina Inc., San Diego, CA). Gene expression analysis was performed according to the manufacturer’s protocol. Five hundred nanograms of total RNA were used for labeling hybridization according to the manufacturer’s protocol. Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc., San Diego, CA), according to the manufacturer's instructions. Initial microarray gene expression data were obtained using the gene expression analysis module of Bead Studio software (version 3.1.3, Illumina Inc., San Diego, CA). To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software. Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.
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| Contributor(s) |
Kim S, Yoon H, Kim Y |
| Citation(s) |
23436614 |
| |
| Submission date |
May 07, 2012 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
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| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
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| Platforms (1) |
| GPL6102 |
Illumina human-6 v2.0 expression beadchip |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE37817 |
DNA methylation and expression profiling study for bladder cancer |
|
| Relations |
| BioProject |
PRJNA163665 |
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