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Dataset results
220 results for “CpG methylation”
Germline CpG methylation signatures in the human population inferred from genetic polymorphism
<p>This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism". </p>
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>
Data from: Methylation of avpr1a in the cortex of wild prairie voles: effects of CpG position and polymorphism
DNA methylation can cause stable changes in neuronal gene expression, but we know little about its role in individual differences in the wild. In this study, we focus on the vasopressin 1a receptor (avpr1a), a gene extensively implicated in vertebrate social behaviour, and explore natural variation in DNA methylation, genetic polymorphism and neuronal gene expression among 30 wild prairie voles (Microtus ochrogaster). Examination of CpG density across 8 kb of the locus revealed two distinct CpG islands overlapping promoter and first exon, characterized by few CpG polymorphisms. We used a targeted bisulfite sequencing approach to measure DNA methylation across approximately 3 kb of avpr1a in the retrosplenial cortex, a brain region implicated in male space use and sexual fidelity. We find dramatic variation in methylation across the avrp1a locus, with pronounced diversity near the exon–intron boundary and in a genetically variable putative enhancer within the intron. Among our wild voles, differences in cortical avpr1a expression correlate with DNA methylation in this putative enhancer, but not with the methylation status of the promoter. We also find an unusually high number of polymorphic CpG sites (polyCpGs) in this focal enhancer. One polyCpG within this enhancer (polyCpG 2170) may drive variation in expression either by disrupting transcription factor binding motifs or by changing local DNA methylation and chromatin silencing. Our results contradict some assumptions made within behavioural epigenetics, but are remarkably concordant with genome-wide studies of gene regulation.
A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health
<p>Higher maternal pre-pregnancy body mass index (ppBMI) is associated with increased neonatal morbidity, as well as with pregnancy complications and metabolic outcomes in offspring later in life. Placenta is a key organ in fetal development and has been proposed to act as a mediator between the mother and different health outcomes in children. The overall aim of the present work is to investigate the association of ppBMI with epigenome-wide placental DNA methylation (DNAm) in 10 studies from the PACE consortium, amounting to 2,631 mother-child pairs. We identify 27 CpG sites at which we observe placental DNAm variations of up to 2.0% per 10 ppBMI-unit. The CpGs that are differentially methylated in placenta do not overlap with CpGs identified in previous studies in cord blood DNAm related to ppBMI. Many of the identified CpGs are located in open sea regions, are often close to obesity-related genes such as GPX1 and LGR4 and altogether, are enriched in cancer and oxidative stress pathways. Our findings suggest that placental DNAm could be one of the mechanisms by which maternal obesity is associated with metabolic health outcomes in newborns and children, although further studies will be needed in order to corroborate these findings.</p> <p>File descriptions:</p> <ul> <li>ppBMI_placenta_unadjustedmodel_NFJ.csv = EWAS summary statistics for the EWAS of ppBMI using the unadjusted model</li> <li>ppBMI_placenta_adjustedmodel_NFJ.csv = EWAS summary statistics for the EWAS of ppBMI using the adjusted model</li> </ul> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a Zenodo DOI generated for you go to ewascatalog.org/upload.</p>
Methylation of p16 CpG Island And Malignant Transformation of Oral Epithelial Dysplasia
ClinicalTrials.gov study NCT00835341. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Methylation of avpr1a in the cortex of wild prairie voles: effects of CpG position and polymorphism
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Spermatozoa RRBS data: Post-Bismark aligned files extracted for the methylation call for every single C in the CpG context of sperm cells of Murrah buffalo bulls under heat stress
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Bisulfite sequencing (RRBS-seq): CpG methylation reports for Australian invasive cane toads
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Data from: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations
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CpG methylation beta values and sample age for the advanced forensic biology lesson
<p>This dataset should be used for the practical of the "Advanced Forensic Biology" lesson. It has been slightly modified from the initial source (see below). It consists of two parts:</p> <p><strong>1) CpG methylation beta values</strong>: tabulated separated methylation beta values in a file called <a href="https://zenodo.org/api/files/9ba3592f-ebe3-442f-9dc6-8b9b29fb170d/cpg_methylation_beta_values.tsv?versionId=5c6942cf-cbfe-4249-a3d9-e2b8b475aa88">cpg_methylation_beta_values.tsv</a>.</p> <p><strong>2) Samples to chronological age </strong>: the relationship between sample identifiers and their chronological age in a tabulated separated file called <a href="https://zenodo.org/api/files/9ba3592f-ebe3-442f-9dc6-8b9b29fb170d/cpg_methylation_sample_age.tsv?versionId=49252b02-9066-4acc-baff-d892320acafc">cpg_methylation_sample_age.tsv</a>.</p> <p><strong>3) CpG identifier to gene symbol and annotation:</strong> a tabulated separated file containing the relationship between CpG island identifier, the corresponding gene and its functional annotation. <a href="https://zenodo.org/api/files/9ba3592f-ebe3-442f-9dc6-8b9b29fb170d/cpg_methylation_cpg_to_annotation.tsv">cpg_methylation_cpg_to_annotation.tsv </a><br> </p> <p> </p> <p><strong>Dataset provenance:</strong></p> <ul> <li>Bocklandt S, Lin W, Sehl ME, Sánchez FJ, Sinsheimer JS, Horvath S, Vilain E. Epigenetic predictor of age. PLoS One. 2011;6(6):e14821. doi: <a href="https://pubmed.ncbi.nlm.nih.gov/21731603/">10.1371/journal.pone.0014821.</a> Epub 2011 Jun 22. PMID: 21731603; PMCID: PMC3120753.</li> <li>GEO link: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28746">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28746</a></li> </ul>
ATTUNE: A Study to Evaluate the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of Intrathecally-Administered ION440 in Participants With Methyl CpG Binding Protein 2 (MECP2) Duplication
ClinicalTrials.gov study NCT06430385. IPD Sharing: YES. Countries: 3. Publications: 0.
Observational Study to Characterize Biomarkers and Disease Progression in Participants With Methyl CpG Binding Protein 2 (MECP2) Duplication Syndrome
ClinicalTrials.gov study NCT06014541. IPD Sharing: NO. Countries: 1. Publications: 0.
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_MBD9]
GEO Series GSE123261. Arabidopsis thaliana. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues
GEO Series GSE15745. Homo sapiens. 1658 samples. Type: Expression profiling by array; Non-coding RNA profiling by array; Methylation profiling by array.
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.
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation
GEO Series GSE256033. Homo sapiens. 79 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing.
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.
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation [ChIP-seq]
GEO Series GSE256030. Homo sapiens. 7 samples. Type: Genome binding/occupancy 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.
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.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.