Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation profiling of normal prostates and prostate cancer metastases [Illumina]

ABSTRACT: DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer Metastases from prostate cancer patients. Normal prostate samples from organ donors

ORGANISM(S): Homo sapiens

SUBMITTER: Martin Aryee

PROVIDER: E-GEOD-38240 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.

Aryee Martin J MJ Liu Wennuan W Engelmann Julia C JC Nuhn Philipp P Gurel Meltem M Haffner Michael C MC Esopi David D Irizarry Rafael A RA Getzenberg Robert H RH Nelson William G WG Luo Jun J Xu Jianfeng J Isaacs William B WB Bova G Steven GS Yegnasubramanian Srinivasan S

Science translational medicine 20130101 169

Human cancers almost ubiquitously harbor epigenetic alterations. Although such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. We carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation "citys ...[more]

PMID: 23345608

Similar Datasets

DNA methylation profiling of normal prostates and prostate cancer metastases [Affymetrix]

Project description:DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer Multiple anatomically distinct metastases from each of five patients. Normal prostate samples from organ donors

2013-02-04 | E-GEOD-38073 | biostudies-arrayexpress

Gene expression profiling of normal prostates and prostate cancer metastases

Project description:Gene expression profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer Multiple anatomically distinct metastases (18) from each of five patients. 21 normal prostate samples from organ donors

2013-02-04 | E-GEOD-38241 | biostudies-arrayexpress

Gene expression profiling of normal prostates and prostate cancer metastases

Project description:Gene expression profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer

2013-02-04 | GSE38241 | GEO

DNA methylation profiling of normal prostates and prostate cancer metastases [Affymetrix]

Project description:DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer

2013-02-04 | GSE38073 | GEO

DNA methylation profiling of normal prostates and prostate cancer metastases [Illumina]

Project description:DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer

2013-02-04 | GSE38240 | GEO

A Basal Stem Cell Signature Identifies Aggressive Prostate Cancer Phenotypes

Project description:Aggressive cancers and normal stem cells often share similar molecular and functional traits. It is unclear if aggressive phenotypes of prostate cancer molecularly resemble normal stem cells residing within the human prostate. We performed high-throughput RNA sequencing on uncultured, highly purified epithelial populations from human prostates obtained after radical prostatectomy. We found the basal population to be defined by genes associated with developmental programs, epigenetic remodeling, and invasiveness. We further generated a 91-gene basal signature and applied it to gene expression datasets from patients with organ-confined or castration-resistant, metastatic prostate cancer. Metastatic prostate cancer was more enriched for the basal stem cell signature than organ-confined prostate cancer. Moreover, histological subtypes within prostate cancer metastases varied in their enrichment of the stem cell signature with small cell neuroendocrine carcinoma being the most stem cell-like. Bioinformatic analysis of the basal cell and two human small cell gene signatures identified a set of E2F target genes common to all three signatures. These results suggest that the most aggressive variants of prostate cancer share a core transcriptional program with normal prostate basal stem cells. Transcriptional analysis of 10 uncultured prostatic basal and luminal populations from either the benign or malignant prostate tissue of 8 human prostate cancer patients by high-throughput RNA-seq

2016-06-01 | E-GEOD-82071 | biostudies-arrayexpress

DNA methylation alterations exhibit striking intra-individual stability and inter-individual heterogeneity across metastatic dissemination

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-02-04 | E-GEOD-38242 | biostudies-arrayexpress

Genomic mapping of ERG, AR, histone H3 monomethyl-K4, histone H3 trimethyl-K4 binding sites in mouse prostates in WT, ERG overexpression, Pten loss mouse prostates

Project description:Translocation of ETS transcription factors including ERG and ETV1 occur in half of all prostate cancers. We generated a mouse model of ERG ovexpression (Rosa26-ERG) which when crossed into prostate specific probasin-Cre, expressed ERG specifically in the prostate. We crossed Rosa26-ERG into Pten flox/flox allele to generate compound GEMM mouse. Here, we determined the genomic binding sites of ERG, AR, and the histone marks H3K4me1 and H3K4me3 that maps enhancers and promoters respectively in the prostates of these mice. The prostate of four six month old mice of each genotype were pooled. The chromatin was isolated and ChIP-Seq performed.

2013-06-13 | E-GEOD-47119 | biostudies-arrayexpress

RNAseq of prostate biopsy tissue from prostate cancer patients on active surveillance over 12 months on different diets (ESCAPE trial)

Project description:There is a need to understand genetic and lifestyle factors that may influence the risk of cancer progression in men who have organ-confined prostate cancer and have chosen a programme of 'active surveillance' as opposed to radical treatment with the associated health risks. Epidemiological studies have suggested that consumption of cruciferous vegetables is associated with reduced risk of developing aggressive prostate cancer. In this study we recruited men on active surveillance for low- to intermediate-risk prostate cancer to determine whether a 12-month dietary intervention can elicit transcriptional or nmetabolic responses in their prostate that would be consistent with a reduction in the risk of progression. We undertook RNAseq on prostate biopsies collected before and after a 12-month intervention with broccoli soups.

2020-01-01 | E-MTAB-6525 | biostudies-arrayexpress

Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer

Project description:High-throughput analyses of concordant gene methylation and expression events were carried out for 91 human prostate specimens, including prostate cancer (T), matched normal adjacent to tumor (AT), and organ donor (OD). Methylated DNA in genomic DNA was immunoprecipitated with anti-methylcytidine antibodies and detected by Affymetrix human whole genome SNP 6.0 chips. Methylated genomic DNA was purified by 5-hmc antibodies and Affymetrix SNP arrays were performed according to the manufacturer's manual. Copy number analysis of Affymetrix human SNP arrays was performed for both 5mc- and genomic DNA of prostate cancer samples. Methylations of genes were called when the allel amplification was reported in 5_mc DNA, and the background of the detection was suppressed by matched DNA sample. we used copy number of each probe set as baseline to detect the enrichment of methylated DNA from the same sample. Therefore, each specimen has two arrays; one is straight copy number (*SNP.CEL), another methylation enriched DNA (*5MC_SNP.CEL). Each CNV probe is based on the design from Affymetrix but no SNP ID was assigned.

2013-08-01 | E-GEOD-45000 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data