Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
429
datasets available to search
ShareScore release 0.9.0
Dataset results
429 results for “Differential methylation”
Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men
<p>The data presented here are the summary statistics for the manuscript, "Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men." The study aims to improve our understanding of prostate cancer disparities between African American and European American men by comparing the DNA methylation features that distinguish tumor and paired, histologically benign tissue from a sample of African American and European American prostate cancer patients. The summary statistics presented here represent the results of a differential methylation analyses comparing tumor and benign tissue in each ancestry group as well as the results of an analysis of differential methylation by ancestry group within each tissue. </p> <p>The files included are: </p> <p>AA_TumorvBenign_Dummy.zip which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in African Americans based on a model that accounts for the paired nature of samples using a series of dummy variables for individual. </p> <p>AA_TumorvBenign_MixedModel.zip which which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in African Americans based on a model that accounts for the paired nature of samples using a linear mixed model that included patient as a random effect. </p> <p>EA_TumorvBenign_Dummy.zip which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in European Americans based on a model that accounts for the paired nature of samples using a series of dummy variables for individual. </p> <p>EA_TumorvBenign_MixedModel.zip which which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in European Americans based on a model that accounts for the paired nature of samples using a linear mixed model that included patient as a random effect. </p> <p>Benign_AncestryCompare_Summary.zip which contains the results of an association analysis between ancestry designation (African American vs European American with African American as the baseline) and individual CpG sites in benign tissue. </p> <p>Tumor_AncestryCompare_Summary.zip which contains the results of an association analysis between ancestry designation (African American vs European American with African American as the baseline) and individual CpG sites in tumore tissue. </p>
Meta-analysis results of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
<p>Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (P<sub>Bonferroni</sub><1.06x10<sup>-7</sup>).</p>
Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"
<p>This data set provides data files and R code to accompany the article <em>Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR</em> published by F1000Research.</p> <p>The data consists of Reduced Representation BS-seq methylation profiles of epithelial populations from the mouse mammary gland, with n=2 biological replicates for each of three cell populations.</p> <p>RNA-seq expression profiles of luminal and basal mammary epithelial populations are also provided.</p> <p>The R code undertakes an differential methylation analysis of the BS-seq profiles and demonstrates a strong negative correlation between the differential methylation and differential expression results.</p>
A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector
<p>This study investigated DNA methylation patterns in two cryptic species (B and Q) of the sweet potato whitefly, <em>Bemisia tabaci</em> (Gennadius), following the acquisition of the tomato yellow curl virus, a single-stranded DNA virus. The methylation levels in genomic features such as promoters, gene bodies, and transposable elements in both cryptic species were described in this study. While overall trends were found to be similar, specific differences in methylation levels were observed. Virus-induced differentially methylated regions (DMRs) were associated with different genes in each cryptic species and were negatively correlated with differential gene expression. These DMRs were analyzed for changes in gene expression and alternative splicing, revealing clusters of hyper- and hypomethylated genes related to virus-vector interactions, immune functions, and detoxification processes. These methylation differences may help explain the distinct biological and physiological traits observed between the B and Q cryptic species.</p>
A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector
Open the record for dataset details and reuse information.
Differentially methylated cytosines in Fragaria vesca
<p>Epigenetic change is considered relatively unstable and short-lived, questioning its contribution to long-term adaptive potential. However, epigenetic modifications can accumulate in the presence of environmental stress, resulting in beneficial epigenetic memories where environments are challenging. Diverging epigenetic memories have been observed across large spatial scales, and can persist through multiple generations even in the absence of the causative environmental stressor. It is unknown, however, to what extent epigenetic variation contributes to fine-scale population structure and evolution. We compared DNA methylation patterns between a steep, altitudinal gradient (<2 km) and a wide spatial gradient (>500 km) using whole genome bisulfite sequencing data from 30 <i>Fragaria vesca</i> plants germinated and grown in controlled conditions. To assess the stability of spatial epigenetic variation in the presence of an environmental stressor, we applied acute drought stress to part of the plants and quantified drought-induced changes in DNA methylation signatures. We find that epigenetic memories and genomic islands of epigenetic divergence arise even at fine spatial scale, and that distinct spatial scales are featured by distinct epigenetic patterns. For example, demethylation of transposable elements consistently occurred at the large but not the fine spatial scale, while methylation differentiation for most biological processes were shared between spatial scales. Acute drought stress did not result in significant epigenetic differentiation. Our results indicate that population history, rather than short-term environmental stress, plays a dominant role in shaping epigenetic signatures. Specifically, repeated historical stress levels associated with heterogeneous environmental conditions may be required for acquiring a stable epigenetic memory and for coping with future environmental change.</p>
Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery
<p>Data Associated with Figures 1 and 2 in Communications Biology Matters Arising: Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery. Original data arising from B. Li et al. <i>Communications Biology</i> <a href="https://doi.org/10.1038/s42003-022-03353-5">https://doi.org/10.1038/s42003-022-03353-5</a> (2022)</p>
Differential methylation analysis in neuropathological confirmed dementia with Lewy bodies
<p>Authors: Paolo Reho, Sara Saez-Atienzar, Sultana Solaiman, Zalak Shah, Ruth Chia, Karri Kaivola, Bryan J. Traynor, Bension S. Tilley, Steve M. Gentleman, Angela K. Hodges, Dag Aarsland, Edwin S. Monuki, Kathy L. Newell, Randy Woltjer, Marilyn S. Albert, Ted M. Dawson, Liana S. Rosenthal, Juan C. Troncoso, Olga Pletnikova, Geidy E. Serrano, Thomas G. Beach, Hariharan P. Easwaran, Sonja W. Scholz</p> <p>Epigenome-wide association study investigating epigenetic modulations in a cohort of neuropathologically confirmed dementia with Lewy bodies cases and neurologically healthy controls.</p>
Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
<p>1. It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments.</p> <p>2. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters (<i>Crassostrea virginica</i>) from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity.</p> <p>3. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression.</p> <p>4. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments.</p> <p>5. An analysis of CpG observed/expected values (CpG O/E ) across the <i>C. virginica</i> genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation, and higher, and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression.</p> <p>6. Taken together, the differential methylation results suggest that only a small portion of the <i>C. virginica</i> genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.</p>
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>
Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes
<p>Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. <em>Eragrostis curvula</em> is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in <em>E</em>. <em>curvula</em> genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.</p>
Differential methylation patterns in apomictic vs. sexual genotypes of the diplosporous grass Eragrostis curvula.
<p>Methylation is an epigenetic mechanism where a methyl group take place over the C5 of cytosine or C6 of adenine repressing or de-repressing genes depending on the context, position (coding or non-coding) and species. Eragrostis curvula is a forage grass that reproduces by apomixis. Increases of the frequency of sexual pistils in facultative genotypes of this grass has been associated to epigenetic changes triggered by different biotic and abiotic stresses. The aim of the present study was to associate differences in the reproductive mode with specific methylated regions and genes contrasting full apomictic, facultative and sexual genotypes using the methylation sensitive technique MCSeEd. The distribution of the differentially methylated positions over the genes shows a peak around the start and stop codon boundaries, hence regulating gene expression mainly through the incorporation of methyl groups on these positions. The main pathways being regulated were ubiquitin and auxins. The methylation pathway itself was also found to be self-regulated since ROS1 and ROS4, the main demethylating genes were found differentially methylated among the different genotypes. Even more, this work allowed us to detect genes regulated by methylation that were previously found differentially expressed in the comparisons between apomictic and sexual genotypes.</p>
Sequencing method matters: Differential performance of DNA methylation data acquisition in epigenetic clock calibration
Open the record for dataset details and reuse information.
Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
Open the record for dataset details and reuse information.
BETA values from DNA methylation (selected differential regions)
Open the record for dataset details and reuse information.
Differentially methylated cytosines in Fragaria vesca
Open the record for dataset details and reuse information.
A Single-center, Prospective Cohort Study on the Differentiation of Benign and Malignant Bile Duct Stenosis Based on Bile and Peripheral Blood cfDNA Methylation Profiles
ClinicalTrials.gov study NCT06115655. IPD Sharing: NO. Countries: 1. Publications: 7.
Circulating Tumor DNA Methylation Test to Differentiate Benign and Malignant Pulmonary Nodules
ClinicalTrials.gov study NCT03181490. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Differential ESR1 promoter Methylation in the peripheral blood of healthy middle-aged and older women- findings from the women 40+ healthy aging study
<p><span><b>Background</b> <a name="_Hlk24051013">Estrogen receptor alpha (ER</a>α) contributes to maintain biological processes preserving health during aging. DNA methylation changes of ERα<i> </i>gene (<i>ESR1</i>) were established as playing a direct role in the regulation of ERα levels. In this study, we hypothesized decreased DNA methylation of <i>ESR1</i> associated with postmenopause, lower estradiol levels and increased age among healthy middle-aged and older women. </span></p> <p><span><b>Methods</b> We assessed DNA methylation of <i>ESR1 </i>promoter region from dried blood spots and estradiol from saliva samples, among 130 healthy women aged 40-73 years. </span></p> <p><span><b>Results</b> We found that postmenopause and lower estradiol levels were associated with lower DNA methylation of a distal regulatory region, but not with DNA methylation of proximal promoters.</span></p> <p><span><b>Conclusion</b> Our results indicate possible adaptive changes of <i>ESR1</i> methylation in women healthy aging.</span></p>
Differential ESR1 promoter Methylation in the peripheral blood of healthy middle-aged and older women- findings from the women 40+ healthy aging study
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.