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203 results for “CpG island”
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
<p>This dataset contains supplemental tables and tracks for the study entitled: "Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation".</p> <ul> <li>Files <ul> <li>PMDs_CGIs.zip <ul> <li>The included files contain</li> <li>Genome positions of detected PMDs with their mean methylation (weighted mean, see Methods)</li> <li>Genome positions of CpG islands with their mean methylation (weighted mean)</li> <li>The "Brinkman" directory contains files from breast cancer data produced in this study</li> <li>The "normals" directory contains files from normal tissues (external data) analyzed in this study</li> <li>The "tumors" directory contains files from tumors (external data) analyzed in this study</li> <li>All genome positions are based on GRCh37/hg19 </li> <li>All files are TAB-delimited text files (.tsv)</li> </ul> </li> <li>DNAme_bigwigs.zip <ul> <li>The included files are BIGWIG files (http://genome.ucsc.edu/goldenPath/help/bigWig.html) for viewing the DNA methylation profiles in a genome browser such as UCSC (http://genome.ucsc.edu). Each file represents a whole-Genome Bisulfite Sequencing (WGBS) DNA methylation profile from one tumor used in this study. The used genome build was GRCh37/hg19. For every CpG with a coverage of at least 4 reads, the DNA methylation value (range: 0-1) is included.</li> </ul> </li> </ul> </li> <li>Methods <ul> <li>Detection of partially methylated domains (PMDs) in all whole-genome bisulfite sequencing (WGBS) methylation profiles throughout this study was done using the MethylSeekR package for R (1). Before PMD calling, CpGs overlapping common SNPs (dbSNP build 137) were removed. The alpha distribution (1) was used to determine whether PMDs were present at all, along with visual inspection of WGBS profiles. After PMD calling, the resulting PMDs were further filtered by removing regions overlapping with centromers (undetermined sequence content).</li> <li>Mean methylation values from WGBS inside CGIs were calculated using the ‘weighted methylation level’ (2).</li> <li>Mean methylation values from WGBS inside PMDs were calculated using the ‘weighted methylation level’ (2). Calculation of mean methylation within PMDs involved removing all CpGs overlapping with CpG island(-shores) and promoters, as the high CpG densities within these elements yield unbalanced mean methylation values, not representative of PMD methylation. </li> </ul> </li> <li>References <ul> <li>(1) Burger, L., Gaidatzis, D., Schübeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Research 41, (2013).</li> <li>(2) Schultz, M. D., Schmitz, R. J. & Ecker, J. R. ’Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends in Genetics 28, 583–585 (2012).</li> </ul> </li> </ul>
Methylation of p16 CpG Island And Malignant Transformation of Oral Epithelial Dysplasia
ClinicalTrials.gov study NCT00835341. IPD Sharing: Not stated. Countries: 1. Publications: 2.
A CpG island-encoded mechanism protects genes from premature transcription termination [SET1_ChIPseq]
GEO Series GSE199801. Mus musculus; Homo sapiens; Drosophila melanogaster. 60 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Hs]
GEO Series GSE104789. Homo sapiens. 14 samples. Type: Methylation profiling by high throughput sequencing.
CpG islands Methylation Profiling by DMH in Epithelial Ovarian Cancer: Screening Set
GEO Series GSE23240. Homo sapiens. 222 samples. Type: Methylation profiling by genome tiling array.
CpG islands recruit a histone H3 lysine 36 demethylase [Agilent data]
GEO Series GSE21201. Homo sapiens. 4 samples. Type: Expression profiling by array.
A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome
GEO Series GSE92254. Homo sapiens. 131 samples. Type: Methylation profiling by high throughput sequencing.
Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes
GEO Series GSE156465. Mus musculus. 28 samples. Type: Other.
The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands.
GEO Series GSE172145. Homo sapiens. 52 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Association between gut microbiota and CpG island methylator phenotype in colorectal cancer [DREAM]
GEO Series GSE237522. Homo sapiens. 148 samples. Type: Methylation profiling by high throughput sequencing.
The CpG Island-Binding Protein SAMD1 Contributes to an Unfavorable Gene Signature in HepG2 Hepatocellular Carcinoma Cells
GEO Series GSE190761. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Methylated CpG island amplification (MCA) microarray analysis of human gastric mucosa and cancer
GEO Series GSE39175. Homo sapiens. 61 samples. Type: Methylation profiling by genome tiling array.
CpG island hypermethylation and CpG-poor region hypomethylation drive gastric cancer risk after Helicobacter pylori eradication
GEO Series GSE296326. Homo sapiens. 16 samples. Type: Methylation profiling by genome tiling array.
Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
GEO Series GSE75346. Homo sapiens. 65 samples. Type: Methylation profiling by high throughput sequencing.
CpG island turnover is associated with evolutionary changes in enhancer activity
GEO Series GSE231307. Mus musculus. 76 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
GEO Series GSE149411. Homo sapiens. 28 samples. Type: Methylation profiling by array.
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [ChIPmentation_TALL]
GEO Series GSE155332. Homo sapiens. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Mm]
GEO Series GSE104781. Mus musculus. 9 samples. Type: Methylation profiling by high throughput sequencing.
BANP opens chromatin and activates CpG island regulated genes [SLAM-Seq]
GEO Series GSE155598. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination [ChIP-Seq]
GEO Series GSE76569. Mus musculus. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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