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.
108
datasets available to search
ShareScore release 0.7.1
Dataset results
108 results for “cytosine methylation”
Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding
<p>TF binding models built by JAMS (https://github.com/csglab/JAMS), ChIP-seq peak files (from ENCODE, Najafabadi et al. 2015, Schmitges et al. 2016, and Imbeault et al. 2017; called by MACS 1.4v), ChIP-seq pulldown and control tags from said peaks, input data for JAMS, and RCADE2 motifs for C2H2 zinc finger proteins. </p>
Museum epigenomics: characterizing cytosine methylation in historic museum specimens
<p>Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post-mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.</p>
Data from: Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe
<p><em><span>Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants <i>Solidago canadensis </i>and <i>S. gigantea</i>,<i> </i>we tested whether such differentiation might have happened through heritable epigenetic changes in cytosine methylation. In a two-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in </span></em><em><i><span>S. canadensis</span></i></em><em><span>, but three genetic clusters in </span></em><em><i><span>S. gigantea</span></i></em><em><span>. </span></em><em><i><span>Solidago canadensis</span></i></em><em><span> showed latitudinal clines in flowering phenology and growth. In </span></em><em><i><span>S. gigantea</span></i></em><em><span>, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, likely through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.</span></em></p>
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>
Data from: Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe
Open the record for dataset details and reuse information.
Museum epigenomics: characterizing cytosine methylation in historic museum specimens
Open the record for dataset details and reuse information.
Differentially methylated cytosines in Fragaria vesca
Open the record for dataset details and reuse information.
Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species
Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.
Effects of temperature treatments on cytosine-methylation profiles of diploid and tetraploid plants of the alpine species Ranunculus kuepferi (Ranunculaceae)
<p>The current dataset refers to the DNA methylation patterns of diploid and tetraploid individuals of <em>Ranunculus kuepferi</em>, obtained with the method of methylation-sensitive AFLPs (MS-AFLPs).</p> <p>The individuals of Ranunculus kuepferi were collected from several locations throughout the distribution of the species in the Alps, transferred to the old Botanical Garden of Göttingen and placed into two climate chambers MC1000E (Snijders Scientific, Tilburg, Netherlands), where the temperature treatment experiments took place. In the first chamber a cold treatment was applied (+7°C day/+2°C night; frost treatment: -1°C cold shocks for three nights per week), while in the second chamber a warm treatment was applied (+15° day/+10°C night).</p> <p>The plants were shifted from one treatment to the other one after the end of the 2016 flowering period and leaf material was collected during the flowering period of 2016 and 2017. This material went through the respective lab procedures in order to obtain the genome-wide patterns of epigenetic variation via MS-AFLPs.</p> <p>The analysis of the electropherograms was conducted with Peakscanner v.2 and fragment scoring was performed with RawGeno 2.0-1 R package. These fragment scoring binary matrices are presented here.</p>
Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species
Open the record for dataset details and reuse information.
Effects of temperature treatments on cytosine-methylation profiles of diploid and tetraploid plants of the alpine species Ranunculus kuepferi (Ranunculaceae)
Open the record for dataset details and reuse information.
Data from: Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome
Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.
Data from: Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)
Open the record for dataset details and reuse information.
Data from: Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome
Open the record for dataset details and reuse information.
The effects of cytosine methylation on general transcription factors
GEO Series GSE64171. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa
GEO Series GSE232935. Neurospora crassa. 31 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability
GEO Series GSE44746. Mus musculus. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other.
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies
GEO Series GSE89913. Arabidopsis thaliana. 2 samples. Type: Methylation profiling by high throughput sequencing.
LATE-REPLICATING HETEROCHROMATIN IS CHARACTERISED BY DECREASED CYTOSINE METHYLATION IN THE HUMAN GENOME (HELP assay)
GEO Series GSE27537. Homo sapiens. 2 samples. Type: Methylation profiling by genome tiling array.
Extensive N4 Cytosine Methylation is Essential for Marchantia Transcriptional Programming and Sperm Function
GEO Series GSE254154. Marchantia polymorpha subsp. ruderalis. 36 samples. Type: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
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.