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503 results for “CpG”
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>
Identification of age-related CpG sites from longitudinal avian methylomes
<p>Sex chromosomes are thought to play an important role in sex-dependent ageing, yet they are neglected in epigenetic aging research. We identified genome-wide age-related CpG (AR-CpG) sites in two avian species (zebra finch and jackdaw) and found AR-CpG sites to be overrepresented on the haploid, female-specific W chromosome in both species, and on the Z chromosome in the zebra finch. </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>
Quantifying CpG variants in a pied flycatcher population
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Identification of age-related CpG sites from longitudinal avian methylomes
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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>
MIMOSA: A resource consisting of improved methylome imputation models increases power to identify CpG site-phenotype associations
<p>MIMOSA DNA methylation prediction models, set up for MWAS. To run MWAS with this resource, see the tutorial here: <a href="https://github.com/ChongWuLab/MIMOSA">https://github.com/ChongWuLab/MIMOSA</a></p>
Phase 1-2 of a CpG-Activated Whole Cell Vaccine Followed by Autologous Immunotransplant for MCL
ClinicalTrials.gov study NCT00490529. IPD Sharing: NO. Countries: 1. Publications: 2.
Immunization With 8 Peptides Mixed With CpG 7909 or Montanide ISA51 in Patients With Metastatic Cutaneous Melanoma
ClinicalTrials.gov study NCT00145158. IPD Sharing: NO. Countries: 1. Publications: 3.
NY-ESO-1 Protein With Montanide and CpG 7909 as Cancer Vaccine in Several Tumors
ClinicalTrials.gov study NCT00299728. IPD Sharing: NO. Countries: 1. Publications: 2.
Immunization With NY-ESO-1 Protein Combined With CpG 7909 in Patients With Prostate Cancer
ClinicalTrials.gov study NCT00292045. IPD Sharing: NO. Countries: 2. Publications: 2.
Immunization With the MAGE-3.A1 Peptide Mixed With the Adjuvant CpG 7909 in Patients With Metastatic Melanoma
ClinicalTrials.gov study NCT00145145. IPD Sharing: NO. Countries: 1. Publications: 3.
CPG 7909 + Local Radiotherapy in Recurrent Low-Grade Lymphomas
ClinicalTrials.gov study NCT00185965. IPD Sharing: Not stated. Countries: 1. Publications: 2.
HepB-CpG Series for Healthcare Workers Who Are Hepatitis B Vaccine Nonresponders
ClinicalTrials.gov study NCT04456504. IPD Sharing: NO. Countries: 1. Publications: 1.
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 Pilot Study of NY-ESO-1b Peptide Plus CpG 7909 and Montanide® ISA-51 in Patients With Cancer.
ClinicalTrials.gov study NCT00199836. IPD Sharing: NO. 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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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.