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| Status |
Public on Jul 25, 2011 |
| Title |
DNA methylation and expression profiling study for prostate cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Methylation profiling by array
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| Summary |
Microarray-based DNA methylation and gene expression profiling was carried out using a panel of prostate cancer cell lines (LNCaP-FGC, DU-145, and PC-3) and the control normal prostate RWPE1 cell line. The identification of prostate cancer-specific methylation markers was based on the following criteria: a difference in DNA methylation level (β) of at least 0.5, and at least a 2-fold difference in expression level between cancer and control cells. Using highly stringent selection criteria, we identified novel hypermethylated genes whose expression was silenced in prostate cancer cells.
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| Overall design |
Genomic DNA was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI). Total RNA was extracted with TRIzol reagent (Life Technologies, NY) according to the manufacturer’s protocol. Methylation patterns were assayed using the genome-wide Illumina Infinium HumanMethylation27 BeadChip array (Illumina Inc., San Diego, CA). Methylation assays were carried out according to the manufacturer’s protocol. Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA). Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value). The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated. For the integrated analysis of global methylation status and gene expression levels, we used the genome-wide HumanHT-12 Gene 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).
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| Contributor(s) |
Kim S, Kim Y, Kim W |
| Citation(s) |
21571867 |
| Submission date |
Aug 03, 2010 |
| Last update date |
Aug 16, 2018 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
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| Phone |
+82-42-879-8107
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| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
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| Department |
Personalized Genomic Medicine Research Center
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| 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 (2) |
| GPL6947 |
Illumina HumanHT-12 V3.0 expression beadchip |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
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| Samples (8)
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| GSM573667 |
Control normal prostate cell line RWPE.1 |
| GSM573668 |
Prostate cancer cell line DU145 [MET] |
| GSM573669 |
Prostate cancer cell line LNCap.FGC [MET] |
| GSM573670 |
Prostate cancer cell line PC3 [MET] |
| GSM573671 |
Control normal prostate cell line RWPE.1 [MET] |
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| Relations |
| BioProject |
PRJNA131259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23388_RAW.tar |
12.0 Mb |
(http)(custom) |
TAR |
| GSE23388_rawdata_expression.txt.gz |
917.4 Kb |
(ftp)(http) |
TXT |
| GSE23388_rawdata_methylation.txt.gz |
575.6 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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