Unknown,Transcriptomics,Genomics,Proteomics

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DNA methylation and expression profiling study for prostate cancer


ABSTRACT: 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. 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).

ORGANISM(S): Homo sapiens

SUBMITTER: Seon-Kyu Kim 

PROVIDER: E-GEOD-23388 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

EFEMP1 as a novel DNA methylation marker for prostate cancer: array-based DNA methylation and expression profiling.

Kim Yong-June YJ   Yoon Hyung-Yoon HY   Kim Seon-Kyu SK   Kim Young-Won YW   Kim Eun-Jung EJ   Kim Isaac Yi IY   Kim Wun-Jae WJ  

Clinical cancer research : an official journal of the American Association for Cancer Research 20110513 13


<h4>Purpose</h4>Abnormal DNA methylation is associated with many human cancers. The aim of the present study was to identify novel methylation markers in prostate cancer (PCa) by microarray analysis and to test whether these markers could discriminate normal and PCa cells.<h4>Experimental design</h4>Microarray-based DNA methylation and gene expression profiling was carried out using a panel of PCa cell lines and a control normal prostate cell line. The methylation status of candidate genes in pr  ...[more]

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