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    Results: 20

    1.

    Epigenomic alterations in localized and advanced prostate cancer

    (Submitter supplied) Here we used Illumina NGS for high-throughput profiling of the DNA methylome in seven human benign prostate tissues, seven human primary prostate cancer and six human castration resistant prostate cancer patient samples. These data were used to profile the CpG cytosine methylation pattern at single base resolution in each sample and to determine differentially methylated cytosines and regions among samples.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by high throughput sequencing
    Platform:
    GPL11154
    20 Samples
    Download data:
    GEO (TXT), SRA SRP016558
    Series
    Accession:
    GSE41701
    ID:
    200041701
    2.

    DNA methylation and expression profiling study for prostate cancer

    (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:
    GEO (TXT)
    Series
    Accession:
    GSE23388
    ID:
    200023388
    3.

    RNA-Seq anlalysis of prostate cancer cell lines using Next Generation Sequencing

    (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:
    GPL9115 GPL9052
    11 Samples
    Download data:
    GEO (BAM), SRA SRP006731
    Series
    Accession:
    GSE29155
    ID:
    200029155
    4.

    Deep sequencing reveals distinct patterns of DNA methylation and transcript isoform regulation in prostate cancer

    (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:
    GEO (BAM, TXT)
    Series
    Accession:
    GSE27619
    ID:
    200027619
    5.

    DNA methylation analysis of prostate cancer cell lines and tissues using Next Generation Sequencing

    (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:
    GEO (TXT), SRA SRP006732
    Series
    Accession:
    GSE27618
    ID:
    200027618
    6.

    Agilent CpG array analysis of Methylplex-library of prostate cancer cell lines

    (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:
    GEO (TXT)
    Series
    Accession:
    GSE27617
    ID:
    200027617
    7.

    Agilent expression analysis of prostate cancer tissue samples

    (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:
    GEO (TXT)
    Series
    Accession:
    GSE27616
    ID:
    200027616
    8.

    Agilent expression analysis of LNCaP cells following 5'aza-treatment

    (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:
    GEO (TXT)
    Series
    Accession:
    GSE25346
    ID:
    200025346
    9.

    Whole Genome Methylation Analysis of Metastatic Castration Resistant Prostate Cancer

    (Submitter supplied) Relatively little is known about how changes in gene copy number (CN) and gene CpG methylation interact to affect specific pathways in metastatic castration-resistant prostate cancer (CRPC). Oligonucleotide array comparative genomic hybridization (aCGH) was performed on DNA isolated from 15 metastatic CRPC samples. Commonly aberrant genes were evaluated in a confirmatory fashion using PCR, aCGH data from primary tumors, and existing CRPC expression data. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array; Methylation profiling by array
    Platforms:
    GPL8490 GPL4091
    30 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE34174
    ID:
    200034174
    10.

    Genome-wide DNA methylation study in bladder cancer

    (Submitter supplied) Genome-wide DNA methylation profiles were determined on a set of fresh 44 bladder cancer tissues using normal blood as control. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Agilent Human CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of bladder cancer along with finding markers for progresssion and early diagnosis.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL4126
    44 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE35824
    ID:
    200035824
    11.

    Discovery of novel hypermethylated gene loci in prostate cancer using genome wide coverage CpG island microarrays

    (Submitter supplied) In order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent human CpG island arrays. We then chose specific genes to validate methylation both in the same cases as were hybridized to the array (using quantitative EpiTYPER analysis) and in an independent series of prostate cancer samples (using MethyLight quantitative methylation specific PCR). more...
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL4126
    20 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE15298
    ID:
    200015298
    12.

    cirDNA methylome analysis in prostate cancer

    (Submitter supplied) DNA modification profiling of circulating DNA (cirDNA) from plasma samples from prostate cancer patients (T2-3N0Mx), benign prostatic hyperplasia and control individuals Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by array
    Platform:
    GPL2040
    118 Samples
    Download data:
    GEO (GPR)
    Series
    Accession:
    GSE36195
    ID:
    200036195
    13.

    Methylation in breast cancer vs. normal tissue

    (Submitter supplied) We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL9767
    10 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE35263
    ID:
    200035263
    14.

    Genome-wide screen for promoter methylation in NSCLC identifies novel methylation markers for multiple malignancies

    (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:
    GEO (CEL)
    Series
    Accession:
    GSE6695
    ID:
    200006695
    15.

    A Genome-wide Screen for Hypermethylated Genes in Lung Cancer

    (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:
    GEO (CEL)
    Series
    Accession:
    GSE5816
    ID:
    200005816
    16.

    Anti-cancer drug sensitive DNA methylation marker research

    (Submitter supplied) Genome wide DNA methylation profiling of normal and colon cancer and assosiation study between anti-cancer drug respond group and non-respond group. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 118 paired anti-cancer drug response tested colon cancer and adjacent normal tissues
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by array
    Platform:
    GPL8490
    248 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE27130
    ID:
    200027130
    17.

    Gene Expression of Prostate Cancer Cells; 22Rv1, DU-145 and LNCaP: 5-Aza-2'-deoxycytidine (DAC) Treatment vs. Control

    (Submitter supplied) Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated three PCa cell lines, 22Rv1, DU-145 and LNCap with the demethylating agent 5-aza 2’–deoxycitidine (DAC) and examined gene expression changes using a custom microarray (GPL16604). more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL16604
    18 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE63196
    ID:
    200063196
    18.

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

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array; Expression profiling by array; Methylation profiling by SNP array
    Platforms:
    GPL4133 GPL6801 GPL13534
    249 Samples
    Download data:
    GEO (CEL, IDAT, TXT)
    Series
    Accession:
    GSE38242
    ID:
    200038242
    19.

    Gene expression profiling of normal prostates and prostate cancer metastases

    (Submitter supplied) Gene expression profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL4133
    39 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE38241
    ID:
    200038241
    20.

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

    (Submitter supplied) DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL13534
    12 Samples
    Download data:
    GEO (IDAT, TXT)
    Series
    Accession:
    GSE38240
    ID:
    200038240

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