221e1b62-f3dd-4f90-bed4-06fc1e75b0f7 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009789 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:DNA methylation is a fundamental epigenetic mark that governs chromatin organization, cell identity, and gene expression. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing of 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are >99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
2022-03-02 | GSE186458 | GEO
Project description:<p>Methylation of cytosines in CpG dinucleotides is an epigenetic mechanism with essential roles in mammalian development. To explore its functions in cellular differentiation, unbiased analysis of CpG methylation by whole genome bisulfite sequencing (WGBS) has been used to characterize epigenetic differences among different human tissues and cell types. Meanwhile, human interindividual variation in DNA methylation that is not cell-type specific has attracted relatively little attention. Systemic interindividual epigenetic variation is important, however, because like genetic variation it is a potential determinant of phenotypic variation and can be assessed in any easily obtainable DNA sample. Since systemic epigenetic variants originate in the preimplantation embryo, their establishment can be influenced by periconceptional environment, and potentially provide information about lifetime risks relevant to global health, obesity, and cancer.</p> <p>We elucidated systemic interindividual variation in CpG methylation in the human genome. We studied brain, heart, and thyroid tissues (representing all three germ layer lineages) from each of 10 donors in the NIH Gene-Tissue Expression (<a href="./study.cgi?study_id=phs000424">GTEx</a>) project. We performed deep whole genome bisulfite sequencing for these 30 samples, achieving a sequencing depth of over 50x coverage per sample. We identified 9,926 correlated regions of systemic interindividual variation (CoRSIVs). These regions, comprising just 0.1% of the human genome, often correlate with one another over long genomic distances, are associated with transposable elements and subtelomeric regions, conserved across various human ethnic groups, and particularly sensitive to periconceptional environment. While genetic variation appears to influence methylation at most CoRSIVs, many show no evidence of genetic influence, suggestive of 'pure' epigenetic variation. At CoRSIVs, interindividual variation in DNA methylation in an easily biopsied tissue predicts expression in other tissues, and genes associated with these loci are implicated in a range of human disorders. In addition to charting a previously unrecognized molecular level of human individuality, this atlas of human CoRSIVs provides a resource for future population-based investigations into how interindividual epigenetic variation modulates risk of disease.</p>
| phs001746 | dbGaP
Project description:DNA methylation is a fundamental epigenetic mark that governs chromatin organization, cell identity, and gene expression. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples.
Replicates of the same cell-type are >99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hyper-methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a novel role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
| EGAS00001006791 | EGA
Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type
2016-02-25 | E-GEOD-66285 | biostudies-arrayexpress
Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line
2016-02-25 | GSE66285 | GEO
Project description:Autism spectrum disorders (ASD), characterized by lack of social and communicative behaviors, have complex etiologies involving multiple genetic and environmental risk factors. Epigenetic information, such as brain DNA methylation patterns, is predicted to reveal insight into the gene networks, cell types, and developmental timing of ASD etiology, but prior methylation studies in ASD have been limited by platform or data integration. Here, we used whole genome bisulfite sequencing (WGBS) to examine DNA methylation genome wide in Brodmann Area 9 of dorsal lateral prefrontal cortex of ASD and Control samples.
2019-09-17 | GSE109875 | GEO
Project description:Changes in epigenetic marks, such as DNA methylation, in cancer subclones may increase their fitness, leading to cancer progression, treatment resistance, and worse prognosis. We have developed DXM, a novel computational method to identify subpopulation methylation events from bisulfite sequencing data of a heterogeneous sample DXM does not require prior knowledge of the number of cell types or what cell types to expect in the sample, and it outperforms existing methods. To further validate our method, we conducted genomic bisulfite sequencing on four primary DLBCL samples, obtaining data from >4.9 million CpGs at 50x average coverage. DXM predictions of subpopulation methylation profiles in these samples were confirmed in FACS-sorted CD4+ and CD19+ cells. Thus, we have developed a method, DXM, that can identify subpopulation methylation profiles in heterogeneous samples
2021-06-04 | GSE130556 | GEO
Project description:To obtain the site-by-site methylation landscape of the infectious spleen and kidney necrosis virus (ISKNV) genome, whole-genome bisulfite sequencing (WGBS) was performed on an ISKNV strain from 3 duplicate samples.
2023-08-23 | GSE241500 | GEO
Project description:We used unbiased whole genome bisulfite sequencing (WGBS) to identify DNA methylation changes in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development. Lgr5-EGFP mice were used to identify ISC populations in the colons. WGBS were performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).
2015-08-25 | E-GEOD-58532 | biostudies-arrayexpress
Project description:Single-cell RNA-sequencing was conducted on specific cell types and heterogeneous viable cells (sorted by FACS) in order to determine a cellular atlas of the normal human prostate.
2018-12-04 | GSE117403 | GEO