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890 results for “nucleosome”
Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor_Figure5e_1
<p>Raw microscopy movies for smFRET experiments with various chromatin templates for Mivelaz M., et al, 2019</p> <p><a href="https://doi.org/10.1016/j.molcel.2019.10.025">https://doi.org/10.1016/j.molcel.2019.10.025</a></p> <p> </p> <p>for Figure 5e (first part)</p> <p>see attached documentation for more details</p>
Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor_Fig.2,3,S3,S4,S7
<p>Raw microscopy movies for colocalization TIRF experiments (Rap1 binding) with various chromatin templates for Mivelaz M., et al, 2019 (<a href="https://doi.org/10.1016/j.molcel.2019.10.025">https://doi.org/10.1016/j.molcel.2019.10.025</a>)</p> <p>for Figures Fig.2,3,S3,S4,S7</p> <p>see attached documentation for more details</p>
Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions.
<p>This dataset includes all time traces from single-molecule experiments as well as raw gel images used in the manuscript. All time traces from single-molecule experiments and can be viewed using vbFRET (https://vbfret.sourceforge.net/). </p>
Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system
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Compromised 2-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers
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Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome
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Data from: Diverse nucleosome site-selectivity among histone deacetylase complexes
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Link to dataset related to article "Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells"
<p>Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of <em>cis</em>-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated <em>cis</em>-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.</p>
The PDBs and maps of DDM1-nucleosome complex
<p>8KCB is DDM1-nucleosome (H2A) complex and 8KCC is DDM1-nucleosome (H2A.W) complex.</p>
Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
<p>Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.</p>
Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products
<p>Optical tweezer data of the mechanical unwrapping of nucleosomes</p>
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
Free DNA and Nucleosome Concentrations in Pathological Pregnancies
ClinicalTrials.gov study NCT01736826. IPD Sharing: Not stated. Countries: 1. Publications: 2.
(Anti-Ribosomal P Protein,Anti-U1 RNP, Anti-Nucleosome and Anti-ds DNA Antibodies) and Relation to Depression and Anxiety in SLE
ClinicalTrials.gov study NCT06255743. IPD Sharing: NO. Countries: 1. Publications: 5.
Reproducibility of Plasma Nucleosomes and Free DNA as Markers for Venous Thromboembolism
ClinicalTrials.gov study NCT01559207. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
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Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
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Data for paper "Detection of new pioneer transcription factors as cell-type specific nucleosome binders"
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Nucleosome Monitoring Relevance for Outcome Prediction in Critically Ill Patients
ClinicalTrials.gov study NCT07184593. IPD Sharing: UNDECIDED. Countries: 0. Publications: 11.
Structure of DNA methyltransferases DNMT3A/DNMT3B bound to a nucleosome [seq]
GEO Series GSE152639. synthetic construct. 20 samples. Type: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
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.