Genome-wide DNA methylation study in bladder cancer
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ABSTRACT:
PROVIDER: PRJNA719302 | ENA |
REPOSITORIES: ENA
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Project description: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. 44 bladder cancer tissues were profiled against commercially available normal human genomic blood DNA (Promega, Madison, WI, USA) as a reference
2012-02-16 | E-GEOD-35824 | biostudies-arrayexpress
Project description: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.
2012-02-16 | GSE35824 | GEO
Project description:Methylation profiling in Bladder cancer : adjacent normal tissue vs bladder tumor tissue
2021-04-03 | GSE171369 | GEO
Project description:Genome-wide DNA methylation study in penile cancer
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Project description:DNA methylation and expression profiling study for bladder cancer
| PRJNA163609 | ENA
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression. 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.
2013-05-03 | E-GEOD-37816 | biostudies-arrayexpress
Project description:It is well established that low-dose Decitabine treatment can sustain long-term antitumor effects by targeting DNA methylation and altering gene expression32. We performed methylated DNA immunoprecipitation (MEDIP) followed by next-generation sequencing in 5637 cells. Daily Decitabine treatment with 100 nM for 72 hr (with or without 100ng/ml cisplatin treatment) reduced the methylation level at CpG-islands in the genome of 5637 cells . However, this low-dose DEC treatment did not cause a significant reduction of DNA methylation in non-CpG islands regions.Our study represents the first detailed analysis of DNA methylome generated by RNA-seq technology in bladder cancer cells treated with low-dose decitabine. This study help to reveal the direct target genes of decitabine in bladder cancer treatement.
2021-04-23 | GSE113537 | GEO
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.
2013-05-03 | GSE37816 | GEO
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression. For the integrated analysis of global methylation status and gene expression levels, we used the genome-wide human-6 v2.0 expression beadchip (Illumina Inc., San Diego, CA). Gene expression analysis was performed according to the manufacturerM-bM-^@M-^Ys protocol. Five hundred nanograms of total RNA were used for labeling hybridization according to the manufacturerM-bM-^@M-^Ys 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). To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software. Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.
2013-05-03 | E-GEOD-37815 | biostudies-arrayexpress
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.
2013-05-03 | GSE37815 | GEO