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5,047 results for “Histone”
Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation
<p>M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)</p> <p>DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)</p> <p>rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1). (Fig. 5)</p>
Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment
<p>Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death.</p> <p> </p>
Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus
<p>Table S4 (Distribution of Orthologous groups) associated with the publication 'Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus' is deposited at Zenodo.</p>
Transcriptome analysis of T47D cells and H2A.J-KO derivatives for the paper entitled: The histone variant H2A.J is enriched in luminal epithelial gland cells
<p>H2A.J is a poorly studied mammalian-specific variant of histone H2A. We used immunohistochemistry to study its localization in various human and mouse tissues. H2A.J showed cell-type specific expression with a striking enrichment in luminal epithelial cells of multiple glands including those of breast, prostate, pancreas, thyroid, stomach, and salivary glands. H2A.J was also highly expressed in many carcinoma cell lines and in particular, those derived from luminal breast and prostate cancer. H2A.J thus appears to be a novel marker for luminal epithelial cancers. Knocking-out the H2AFJ gene in T47D luminal breast cancer cells reduced the expression of several estrogen-responsive genes which may explain its putative tumorigenic role in luminal-B breast cancer.</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>
Ultra-Accurate Correlation Between Precursor and Fragment Ions in Two-lDimensional Mass Spectrometry: Acetylated vs. Trimethylated Histone Peptides
<p>Two-dimensional mass spectrometry (2D MS) is a method<br> for tandem<br> mass spectrometry in which precursor and fragment ions are correlated<br> by manipulating ion radii rather than by ion isolation. A 2D mass<br> spectrum contains the fragmentation patterns of all analytes in a<br> sample, acquired in parallel. We report ultrahigh-resolution narrowband<br> 2D mass spectra of a mixture of two histone peptides with the same<br> sequence, one of which carries an acetylation and the other a trimethylation<br> (m/z 0.006 difference). We reduced<br> the distance between data points in the precursor ion dimension and<br> compared the accuracy of the precursor-fragment correlation with the<br> resolving power. We manage to perform label-free quantification on<br> the histone peptide mixture and show that precursor and fragment ions<br> can be accurately correlated even though the precursor ions are not<br> resolved. Finally, we show that increasing the resolution of a 2D<br> mass spectrum in the precursor ion dimension too far can lead to a<br> decline in the signal-to-noise ratio.</p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Crosstalk assessment for multi-colour immunofluorescence of Histone 3 and Polymerase II post-translational modifications in pluripotent zebrafish embryos
<p>Microscopy images recorded to assess the extent of crosstalk from the detection channels of H3K27ac and recruited RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1) to the detection channel of elongating RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1). Sample preparation and image recording was carried out jointly by Süheyla Eroğlu-Kayikci, Elisa Kämmer, and Lennart Hilbert.</p>
Data from: Histone acetyltransferases and external demands influence task switching in Temnothorax ants
<p><span>In social hymenopterans, workers specialize on different tasks. Whether a worker nurses the brood or forages is influenced by the responsiveness for task-related cues which in turn is determined by gene expression. Task choice is dynamic and changes throughout a worker's life, e.g. with age or in response to increased demands for certain tasks. Behavioral switches require the ability to adjust gene expression but the mechanisms regulating such transcriptional adaptations remain elusive. We investigated the role of histone acetylation in task specialization and behavioral flexibility in <em>Temnothorax longispinosus</em> ants. By inhibiting p300/CBP histone acetyltransferases (HAT) and manipulating colony composition, we found that HAT inhibition impairs the ability of older workers to switch to brood care. Yet, HAT inhibition increased the ability of young workers to accelerate their behavioral development and switch to foraging. Our data suggest that HAT in combination with social signals indicating task demands play an important role in modulating behavior. Elevated HAT activity may contribute to keeping young brood carers from leaving the nest, where they would be exposed to high mortality. These findings shed light on the epigenetic processes underlying behavioral flexibility in animals and provide insight into the mechanisms of task specialization in social insects.</span></p>
The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea
<p>The shown folders contain the molecular dynamics simulation data, used tools, and scripts for the study of "The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea". The simulation data includes the force field and simulation setup for both AWSEM-MD and atomistic MD in OpenMM, the data analyses that are presented in the related paper, and the representative conformations from each simulation. Due to the large file size, the original trajectory files are available upon separate request.</p> <p>The tools and scripts folder includes the specific version of the AWSEM model, implemented in the LAMMPS package, and the scripts used to analyze the simulations. For detailed instructions on using AWSEM model, please refer to our Github: <a href="https://github.com/adavtyan/awsemmd/wiki">https://github.com/adavtyan/awsemmd/wiki</a>. For detailed instructions on using the LAMMPS package, please refer to <a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>. For detailed instructions on using the OpenMM package, please refer to <a href="https://openmm.org/">https://openmm.org/</a>. For any questions about using this data repository, please feel free to contact the author.</p> <p> </p> <p> </p>
Histones with an unconventional DNA binding mode are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus
<p>Original Microscopy images for the publication "Histones with an unconventional DNA binding mode are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus". Published title might change.</p>
Effect of the histone deacetylase inhibitor Trichostatin A on facial development in cichlid fishes
<p>A central question in biology is the molecular origins of phenotypic diversity. While genetic changes are key to the genotype-phenotype relationship, alterations to chromatin structure and the physical packaging of histone proteins may also be important drivers of vertebrate divergence. We investigate the impact of such an epigenetic mechanism, histone acetylation, within a textbook example of an adaptive radiation. Cichlids of Lake Malawi have adapted diverse craniofacial structures, and here we investigate how histone acetylation influences morphological variation in these fishes. Specifically, we assessed the effect of inhibiting histone deacetylation using the drug trichostatin A (TSA) on developing facial structures. We examined this during three critical developmental windows in two cichlid species with alternate adult morphologies. Exposure to TSA during neural crest cell (NCC) migration and as post-migratory NCCs proliferate into the pharyngeal arches resulted in significant changes in lateral and ventral shape in <em>Maylandia</em>, but not in <em>Tropheops</em>. This included an overall shortening of the head, widening of the lower jaw, and steeper craniofacial profile, all of which are paedomorphic morphologies. In contrast, treatment with TSA during early chondrogenesis did not result in significant morphological changes in either species. Together, these data suggest a sensitivity to epigenetic alterations that are both time- and species-dependent. We find that morphologies are due to non-autonomous or potentially indirect effects on NCC development, including in part a global developmental delay. Our research bolsters the understanding that proper histone acetylation is essential for early craniofacial development and identifies a species-specific robustness to developmental change. Overall, this study demonstrates how epigenetic regulation may play an important role in both generating and buffering morphological variation.</p>
Dietary Histone Deacetylase Inhibitors (HDAC)
ClinicalTrials.gov study NCT01543074. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Exploratory Evaluation of AR-42 Histone Deacetylase Inhibitor in the Treatment of Vestibular Schwannoma and Meningioma
ClinicalTrials.gov study NCT02282917. IPD Sharing: NO. Countries: 1. Publications: 2.
Effect of the histone deacetylase inhibitor Trichostatin A on facial development in cichlid fishes
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Supplementary materials from: Histone deacetylase 2 and 3 of Sarcoptes scabiei: Characterization of a potential drug target
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Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
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Data from: Histone acetyltransferases and external demands influence task switching in Temnothorax ants
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Histone H1.2 dependent translocation of poly (ADP-ribose) initiates parthanatos
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Histone acetyltransferase p300/CBP regulates reproductive diapause via the juvenile hormone pathway in the cabbage beetle, Colaphellus bowringi
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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.