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35 results for “population epigenetics”
Supporting data for "A simple ATAC-seq protocol for population epigenetics"
<p>This is supporting data for an article in which we describe a protocol for the generation of sequence-ready libraries for population epigenomics studies. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size, and it requires little molecular biology handling expertise.</p> <p>In "Agarose picture.Tif" the left lane shows the 100 bp size marker, first 10 bands from down to top: 100bp, 200bp, 300bp, 400bp, 500bp, 600bp, 700bp, 800bp, 900bp and 1kbp.</p> <p>Produced at IHPE (http://ihpe.univ-perp.fr/)</p>
Data from: Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept
Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
Data from: Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations
Background: The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations. Results: The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We used methylation sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) techniques, to assess the methylation status of random genomic CCGG sites and CCGG sites flanking transposable elements (TEs), respectively. Both techniques were applied to the DNA of 50 emmer accessions which were collected from five different geographically isolated regions. In order to ensure the assessment of heritable epigenetic variation, all accessions were grown under common garden conditions for two generations. In all accessions, the difference in methylation levels of CCGG sites, including CCGG sites that flanked TEs, were not statistically significant and relatively high, ranging between 46 and 76 %. The pattern of methylation was significantly different among accessions, such that clear and statistically significant population-specific methylation patterns were observed. Conclusion: In this study, we have observed population-unique heritable methylation patterns in emmer wheat accessions originating from five geographically isolated regions. Our data indicate that methylation-based epigenetic diversity might be eco-geographically structured and might be partly determined by climatic and edaphic factors.
Data from: Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure
<p><strong>General information</strong></p> <p>This deposition contains the datasets that were used in the statistical analysis of the manuscript entitled <strong>Traces of genetic but not epigenetic adaptation in the invasive goldenrod <em>Solidago canadensis</em> despite the absence of population structure </strong>published in Frontiers in Ecology and Evolution (doi: <a href="https://doi.org/10.3389/fevo.2022.856453">10.3389/fevo.2022.856453</a>).</p> <p><strong>Uploaded files</strong></p> <ul> <li><strong>README</strong> file to explain the datasets</li> <li><strong>AFLP/MSAP metadata</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLPMSAP_meta_data.txt</li> <li><strong>AFLP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLP_scoring_data.txt</li> <li><strong>MSAP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data.txt</li> <li><strong>MSAP mix1-scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data_mix1.txt</li> <li>All files were combined in a <strong>.zip file</strong></li> </ul>
Data from: Genetic and epigenetic differentiation between natural Betula ermanii (Betulaceae) populations inhabiting contrasting habitats
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Data from: Fine-scale population epigenetic structure in relation to gastro-intestinal parasite load in red grouse (Lagopus lagopus scotica)
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Data from: Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations
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Data from: Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept
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Data from: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expression
Many species exhibit transgenerational plasticity by which environmental cues experienced by either parent can be transmitted to their offspring, resulting in phenotypic variants in offspring to match ancestral environments. However, the manner by which paternal experiences affect offspring plasticity through epigenetic inheritance in animals generally remains unclear. In this study, we examined the transgenerational effects of population density on phase-related traits in the migratory locust Locusta migratoria. Using an experimental design that explicitly controls genetic background, we found that the effects of crowd or isolation rearing on phase plasticity could be inherited to the offspring. The isolation of gregarious locusts resulted in reduced weight in offspring eggs and altered morphometric traits in hatchlings, whereas crowding of solitarious locusts exhibited opposite effects. The consequences of density changes were transmitted by both maternal and paternal inheritance, although the expression of paternal effects was not as pronounced as that of maternal effects. Prominent expression of heat-shock proteins (Hsps), such as Hsp90, Hsp70, and Hsp20.6, could be triggered by density changes. Hsps were significantly upregulated upon crowding but downregulated upon isolation. The variation in parental Hsp expression was also transmitted to the offspring, in which the pattern of inheritance was consistent with that of phase characteristics. These results revealed a paternal effect on phase polyphenism and Hsp expression induced by population density, and defined a model system that could be used to study the paternal epigenetic inheritance of environmental changes.
Data from: The evolution of epigenetically-mediated adaptive transgenerational plasticity in a subdivided population
Transgenerational plasticity (TGP) occurs when offspring exhibit plasticity in traits induced by the environments experienced by their parents, and represents a non-genetic mechanism of inheritance. Evidence that traits can be transmitted to future generations by means other than genetic inheritance has caused a surge of interest in epigenetic inheritance, but evidence for epigenetic modifications being both adaptive and heritable remains scarce. What features would make a species most prone to evolve a system of epigenetically-mediated adaptive TGP? Here we use population-genetic models modified to include epigenetic induction and inheritance to investigate if and when epigenetically-mediated adaptive TGP would be expected to evolve for a population subdivided between two habitats connected by migration. We show that differences in the direction of selection between the two habitats drives the evolution of epigenetically-mediated adaptive TGP. With low migration, the strength of indirect selection in favour of epigenetically-mediated adaptive TGP increases with migration rate. Yet, with higher migration, the opposite trend is observed. We predict that species subdivided between habitats that differ in the direction of selection with moderate migration rates between the habitats would be most likely to evolve epigenetically-mediated adaptive TGP if costs of producing such systems are not too high.
Epigenetic diversity underlying seasonal and annual variations in brown planthopper (BPH) populations as revealed by methylation-sensitive restriction assay
<p>Raw data files for the image analysis.</p>
Data from: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expression
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Data from: The evolution of epigenetically-mediated adaptive transgenerational plasticity in a subdivided population
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Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [ChIP-Seq]
GEO Series GSE226682. Arabidopsis thaliana. 139 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
DNA Methylation Profiling at Base-Pair Resolution Reveals Unique Epigenetic Features of Early-Onset Colorectal Cancer in Underrepresented Populations
GEO Series GSE284325. Homo sapiens. 16 samples. Type: Methylation profiling by high throughput sequencing.
Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [scRNA-Seq]
GEO Series GSE171530. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Epigenetic drugs selectively target a population of AML cells which are positive for CD123 cell surface markers and are chemoresistant I
GEO Series GSE108142. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes
GEO Series GSE133502. Potamopyrgus antipodarum. 9 samples. Type: Methylation profiling by high throughput sequencing.
Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [ATAC-Seq]
GEO Series GSE171529. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [Bisulfite-seq]
GEO Series GSE226560. Arabidopsis thaliana. 88 samples. Type: Methylation profiling by high throughput sequencing.
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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.