GEO DataSets

(Submitter supplied) Two prostate immortalized cell lines, 267B1, RWPE-1, Ml-csv40, and five prostate cancer cell lines, PC3, PC3M, PC3M-Pro4, PC3M-LN4 and LNCaP are included in this experiment. Their methylation profile are detected using human promoter array (v11). mRNA expression level are profiled with Affymetrix U133A Arrays for 267B1 and PC3M. Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL864 GPL80 GPL96

14 Samples

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(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL9115

11 Samples

Download data: BAM

(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

39 Samples

Download data: BAM, TXT

(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2) from fifty nanograms of genomic DNA using Methylplex-Next Generation Sequencing (M-NGS). A Hidden Markov Model (HMM)-based algorithm previously used for Chip-Seq data analysis(http://www.sph.umich.edu/csg/qin/HPeak) was used to locate peaks from mapped reads obtained in each sequencing run. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9115

9 Samples

Download data: TXT

(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

2 Samples

Download data: TXT

(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

13 Samples

Download data: TXT

(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

4 Samples

Download data: TXT

(Submitter supplied) Effects of sulforaphane and 3,3’-diindolylmethane on genome-wide promoter methylation in normal prostate epithelial cells and prostate cancer cells This study was undertaken to determine the genome-wide effects of sulforaphane (SFN) and 3,3’-diindolylmethane (DIM) on promoter methylation in normal prostate epithelial cells and prostate cancer cells. Nimblegen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array was used in this study. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL17148

27 Samples

Download data: GFF, PAIR

(Submitter supplied) Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35 K longmer oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomers, were detected. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5046

11 Samples

Download data: TXT

(Submitter supplied) Transcriptional silencing associated with aberrant promoter hypermethylation is a common mechanism of inactivation of tumor suppressor genes in cancer cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9452

8 Samples

Download data: XLS

(Submitter supplied) Background: Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL

(Submitter supplied) Abstract Background: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor-type specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

42 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL6947 GPL8490

8 Samples

Download data: TXT

(Submitter supplied) The prostate represents a complex mix of cell types and there is a need to analyze distinct cell populations to better understand their potential interactions. This study of cell-type specific gene expression patterns will contribute to understanding of how tumor epithelial cells may be affected by adjacent interstitial stromal cells within the tumor microenvirnonment. LCM and microarray analysis were used to identify gene expression patterns in prostate cancer epithelial and interstitial stromal cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

6 Samples

Download data: CEL, CHP

(Submitter supplied) Melanoma progression model:DAC-mediated gene expression Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1440

Platform:

GPL80

6 Samples

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(Submitter supplied) Melanoma progression model Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL80

6 Samples

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Analysis of a poorly tumorigenic melanoma cell line and its 3 highly aggressive derivative lines after treatment with 2'-deoxy-5-azacytidine (DAC), a DNA methyltransferase inhibitor. Results suggest multiple markers for melanoma progression that are regulated by DNA methylation.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 agent, 4 cell line, 2 cell type sets

Platform:

GPL80

Series:

GSE1793

6 Samples

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(Submitter supplied) Genome wide DNA methylation profiling of normal and tumor prostate samples, as well as cultured primary prostate cells overexpressing DNA Methyltransferases (DNMTs) and EZH2 Candidate gene based studies have identified a handful of aberrant CpG DNA methylation events in prostate cancer. However, DNA methylation profiles have not been compared on a large scale between prostate tumor and normal prostate, and the mechanisms behind these alterations are unknown. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

193 Samples

Download data: TXT

(Submitter supplied) A microarray-based strategy using digestion with the methylation-sensitive restriction enzyme HpaII, ligation, and PCR, was performed to assess the DNA methylation status of promoter regions in Six human cervical adenocarcinomas (ACA) and four squamous cell carcinomas (SCC). Two array platforms were used; an array of 11,994 ~1.5kb PCR products from 10,445 promoter regions, and an array of 355,264 oligonucleotides for 18,212 HpaII fragments in 12,617 promoter regions. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL6442 GPL6441 GPL8286

24 Samples

Download data: TXT