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4,916 results for “DNA methylation”
MeDeMo - a dependency model for DNA methylation-aware transcription factor binding predictions
<p>The uploaded <em>fasta </em>files contain extended reference genomes for three cell lines HepG2, GM12878, K562 (ENCODE) and two primary liver hepatocyte samples from the german epigenomics consortium (DEEP). The extended reference genomes contain information on DNA methylation in a CpG context. They can be used as input for <em>MeDeMo</em>, a tool to infer transcription factor binding sites incorporating not only sequence specificity but also DNA methylation. <em>MeDeMo </em>is available online at: <a href="http://www.jstacs.de/index.php/MeDeMo">http://www.jstacs.de/index.php/MeDeMo</a>.</p> <p>We considered the files ENCFF279HCL and ENCFF835NTC for GM12878, ENCFF867JRG and ENCFF721JMB for K562 as well as ENCFF064GJQ and ENCFF369YQW for HepG2. From DEEP, we considered samples 41_Hf01 and 41_Hf03 which are available through the International Human Epigenomics Consortium (IHEC).</p> <p>In addition, we provide all models trained using the mentioned data sets as well models for and motifs from genome wide predictions.</p>
Residential greenness-related DNA methylation changes
<p>EWAS of residential greenness in the population-representative Swiss samples.</p> <p>EWAS of two different residential greeness are included here: </p> <ul> <li>NDVI of 500 m circular buffer surrounding residential address (ewas_final_truncate_green500.csv)</li> <li>NDVI of 30x30m cell surrounding residential address (ewas_final_truncate_green30.csv)</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> <p> </p>
Investigating the DNA methylation profile of e-cigarette use
<p>EWAS of smoking (vs. non-smoking) in SEE-Cigs study (smvsnon_mainmodel.csv)</p> <p>EWAS of e-cigarette use (vs. smoking) in SEE-Cigs study (vapevssm_mainmodel.csv)</p> <p>EWAS of e-cigarette use (vs. non-smoking) in SEE-Cigs study (vapevsnon_mainmodel.csv)</p>
Maternal Dietary Glycemic Index and Glycemic Load in Pregnancy and Offspring Cord Blood DNA Methylation
<p><strong>Abstract</strong></p> <p><strong>Objective</strong>: Suboptimal nutrition in pregnancy is associated with worse offspring cardiometabolic health. DNA methylation may be an underlying mechanism. We meta-analyzed epigenome-wide association studies (EWASs) of maternal dietary glycemic index and load with cord blood DNA methylation.</p> <p><strong>Research Design and Methods</strong>: We calculated maternal glycemic index and load from food frequency questionnaires, and ran EWASs on cord blood DNA methylation in 2003 mother-offspring pairs from three cohorts. Analyses were additionally stratified by maternal BMI categories. We looked-up the findings in EWASs of maternal glycemic traits and BMI, and in EWASs of birthweight and child BMI. We examined associations with gene expression in child blood in the online Human Early Life Exposome eQTM catalogue and in 223 adipose tissue samples.</p> <p><strong>Results</strong>: Maternal glycemic index and load were associated with cord blood DNA methylation at 41 cytosine-phosphate-guanine sites (CpGs, P<1.17x10<sup>-7</sup>), mostly in mothers with overweight/obesity. We did not observe overlap with CpGs associated with maternal glycemic traits, BMI or child birthweight or BMI. Only DNA methylation at cg24458009 and cg23347399 was associated with expression of <em>PCED1B</em> and <em>PCDHG</em>, respectively, in child blood, and DNA methylation at cg27193519 was associated with expression of <em>TFAP4</em>, <em>ZNF500</em>, <em>PPL</em> and <em>ANKS3</em> in child subcutaneous adipose tissue.</p> <p><strong>Conclusions</strong>: We observed multiple associations of maternal glycemic index and load during pregnancy with cord blood DNA methylation, mostly in mothers with overweight/obesity; some of these CpGs were associated with gene expression. Additional studies are required to further explore functionality, uncover causality, and study pathways to offspring health.</p>
Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), ATXN1, SLC17A6, NR4A2, and PTPRN2 in cortical neurons
<p>Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell-type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this first genome-wide analysis of DNA methylation in an enriched neuronal population from PD post-mortem parietal cortex, we report sex-specific PD-associated methylation changes in <em>PARK7</em> (DJ-1), <em>SLC17A6</em> (VGLUT2), <em>PTPRN2</em> (IA-2β), <em>NR4A2</em> (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.</p>
Code and data for "Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer".
<p>Code and data for "<strong>Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer</strong>".</p> <ul> <li> <p>The publicly available datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository (<a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a>) and UCSC Xena Browser (TCGA, <a href="https://xena.ucsc.edu/">https://xena.ucsc.edu/</a>).</p> </li> </ul>
BETA values from DNA methylation (selected differential regions)
<p><span>Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the "biologically embedding" of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation 850K BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with, versus those without, neglectful behavior (n = 51 vs 87) that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the </span><span>α</span><span> = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development, and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and Alzheimer's disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.</span></p>
Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models (NMR datasets, maternal plasma and infant brain)
<p>Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. Ultimately, maternal obesity altered infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors. </p>
Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination
<p>Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (<em>Alligator mississippiensis</em>), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and 4 test samples) and past incubation temperature with a mean absolute error of 1.2˚C (in 4 test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity. </p>
Investigating food production-associated DNA methylation changes in paleogenomes: lack of consistent signals beyond technical noise
<p>The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarchaeological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherer (HGs) and 21 Neolithic farmer (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1x-58x (median=9x). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analysing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers vs. farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.</p>
An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer
<p>Supplemental data for the paper titled "An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer"</p>
EWAS results "Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer"
<p>Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts.</p> <p>DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an Epigenome Wide Association Study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip, and subject as random effect.</p> <p>The full analyses results are deposited here.</p>
Cross-species and tissue imputation of species-level DNA methylation samples
<p>Imputed dataset of DNA methyation samples representing the predicted mean methylation of a species and tissue type. </p>
Impact of exposure to second-hand smoke during childhood on blood DNA methylation
<p>Meta-analysis results for CpGs associated with household postnatal exposure to second hand smoke (SHS). Cohorts order are GenR, PIAMA, HELIX, BAMSE_Medall, BAMSE_EpiGene, and ALSPAC. Effect size represents the change in DNAm by number of household smokers (from 0 smokers to 2 smokers or more). Gene and CpG Island relative position are indicated (TSS200 is the region from Transcription start site (TSS) to − 200 nt upstream of TSS; TSS1500 covers − 200 to − 1500 nt upstream of TSS; S_Shore corresponds to the 2 kb regions immediately downstream of the CpG island; N_Shore corresponds to the 2 kb regions immediately upstream of the CpG island). Chr stands for Chromosome, SE stands for standard error, I2 stands for heterogeneity index, and FDR stands for False Discovery Rate. (DNA data obtained through Iluumina 450K array profiling)</p>
Characterization of DNA methylation reader proteins of Arabidopsis thaliana
<p>Genomic regions of interest from the study "Characterization of DNA methylation reader proteins of Arabidopsis thaliana". </p>
Supplementary Table S2 - Stability of Blood DNA Methylation Across Two Timepoints in Three Cohorts
<p>Supplementary Table S2 from "Stability of Blood DNA Methylation Across Two Timepoints in Three Cohorts", published in Biomedicines.</p> <p><span>This research was funded by the National Science Centre, Poland, grant numbers 2017/26/E/NZ5/00851 (K.W.) and 2020/39/D/NZ5/02720 (J.K.N.).</span></p>
Dynamic changes in DNA methylation during postnatal development in zebra finches (Taeniopygia guttata) exposed to different temperatures
<p>Epigenetic changes associated with early life conditions are known to play a significant role in shaping the adult phenotype. Studies of DNA methylation in wild animals are lacking, yet are important for understanding the fitness consequences of environmentally induced epigenetic change. In our study, we quantified variation in DNA methylation in wild, post-hatch zebra finches Taeniopygia guttata developing at seasonally variable temperatures in the Australian desert. We also compared variation in DNA methylation among captive zebra finch siblings raised in temperature controlled 'hot' or 'cool' rooms. We detected an increase in genome-wide levels of DNA methylation between day 3 and day 11 of post hatch development in wild zebra finches. In the wild, ambient temperatures were also found to affect genome-wide levels of DNA methylation and plasticity in the methylation state of individual loci. Family effects had a significant influence on DNA methylation throughout our study, and while we did not detect an effect of temperature on DNA methylation levels in non-related captive birds, our sibling pair analyses revealed that within families, elevated temperatures were associated with higher levels of DNA methylation. Our findings suggest a wide window in early development during which climatically induced variation in DNA methylation could occur. Further work is necessary to understand the potential for such variation to promote ecologically relevant variation in wild birds.</p>
Analysis of DNA methylation profile of Korean chronic lymphocytic leukaemia (CLL) patients with MeDIP-Seq
<p>In this study, we performed genome-wide methylation profiling of eight CLL patients and five control subjects, in an Asian cohort. Methyl-CpG-binding domain sequencing (MBD-Seq) was used as the profiling method. Differential methylation analysis identified a number of differentially methylated regions (DMRs) and genes (DMGs). More regions were hypomethylated than were hypermethylated. Promoters contained the highest proportion of DMRs, while distal intergenic and intron regions contained the largest number of DMRs. Gene Ontology, pathway analysis, and network-based prioritization of DMGs were also performed.</p>
Data from: Genome-wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird
Individuals often differ in their ability to cope with challenging environmental and social conditions. Evidence from model systems suggests that patterns of DNA methylation are associated with variation in coping ability. These associations could arise directly if methylation plays a role in controlling the physiological response to stressors by, among other things, regulating the release of glucocorticoids in response to challenges. Alternatively, the association could arise indirectly if methylation and resilience have a common cause, such as early life conditions. In either case, methylation might act as a biomarker for coping ability. At present, however, relatively little is known about whether variation in methylation is associated with organismal performance and resilience under natural conditions. We studied genome-wide patterns of DNA methylation in free-living female tree swallows (Tachycineta bicolor) using methylated DNA immunoprecipitation (MeDIP) and a tree swallow genome that was assembled for this study. We identified areas of the genome that were differentially methylated with respect to social signal expression (breast brightness) and physiological traits (ability to terminate the glucocorticoid stress response through negative feedback). We also asked whether methylation predicted resilience to a subsequent experimentally imposed challenge. Individuals with brighter breast plumage and higher stress resilience had lower methylation at differentially methylated regions across the genome. Thus, widespread differences in methylation predicted both social signal expression and the response to future challenges under natural conditions. These results have implications for predicting individual differences in resilience, and for understanding the mechanistic basis of resilience and its environmental and social mediators.
Genetic variation influencing DNA methylation provides new insights into the molecular pathways regulating genomic function - Selected Supplementary Tables
<p><strong>Selected Supplementary Tables - ST5, 7, 8 and 9</strong></p> <p><strong>Supplementary Table 5. Cosmopolitan results. </strong>Cosmopolitan SNP-CpG associations identified through genome-wide association amongst Europeans and South Asians.</p> <p><strong>Supplementary Table 7. Cross-tissue replication.</strong> Results for further testing of the 11,165,559 cosmopolitan SNP-CpG associations identified (by genome-wide association in blood), in 4 isolated white cell subsets (CD4+ lymphocytes, CD8+ lymphocytes, monocytes and neutrophils), in adipocytes isolated from subcutaneous adipose tissue or visceral adipose tissue, and in whole adipose tissue.</p> <p><strong>Supplementary Table 8. Conditional analysis.</strong> Results of conditional analysis to identify SNPs independently associated with each of the ~360K CpG sites tested. </p> <p><strong>Supplementary Table 9. Sentinel SNPs and CpGs.</strong> Results of R2 pruning and locus merging to identify discrete genetic and methylation loci that are associated, and their respective sentinel SNPs and sentinel CpG sites. </p> <p>Other files (e.g. annotation files and 'intermediate' processing files) referenced in our code are also provided. </p> <p> </p>
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.