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607 results for “Histone modifications”
Nanoscale Shape-Dependent Histone Modifications
<p>Recent observations suggest a role for complex nanoscale particulate shape in regulation of specific immune-related cellular and in vivo processes. We suspect that cellular recognition of nanostructure architecture could involve non-molecular inputs, including cellular transduction of nanoscale spatially resolved stresses induced by complex shape. Here we report nanoscale shape-dependent control of the cellular epigenome. ChIP-Seq sequencing datasets are provided.</p>
Supporting data for "Chromatin conformation and histone modification profiling across human kidney anatomic regions"
<p>Here we deposit supporting data for our manuscript entitled "Chromatin conformation and histone modification profiling across human kidney anatomic regions".</p> <ul> <li>donor_info.pdf: Additional clinical information of the donor involved in the study</li> <li>Large zip files with names starting as "hic": Juicer Hi-C outputs aligned with hg38 genome <ul> <li>Note: hg19 alignment outputs are available at GEO.</li> </ul> </li> <li>hg19_loop_domain.zip: Hi-C chromatin contact domain finding results with Arrowhead and chromatin loop finding results with HiCCUPs (implemented in Juicer tools), aligned with hg19 genome</li> <li>hg38_loop_domain.zip: Hi-C chromatin contact domain finding results with Arrowhead and chromatin loop finding results with HiCCUPs (implemented in Juicer tools), aligned with hg38 genome</li> <li>CUTRUN_peak_hg19.tar.gz: CUT&RUN peaks.stringent.bed data outputs generated by hg19 alignment</li> <li>CUTRUN_peak_hg38.tar.gz: CUT&RUN peaks.stringent.bed data outputs generated by hg38 alignment</li> <li>CUTRUN_bigwig_hg38.tar.gz: CUT&RUN bigwig outputs generated by hg38 alignment <ul> <li>Note: hg19 alignment outputs are available at GEO.</li> </ul> </li> <li>CUTRUN_overlapped_peaks.xlsx: Overlaps between H3K27me3 and H3K4me3 in each anatomical region. Peaks were loaded from ‘.peaks.stringent.bed’ files in R and converted to GRanges objects using package ‘GenomicRanges’. R function ‘intersect’ was used to calculate the overlap between two GRanges objects, represented as each row in the table. <ul> <li>Here we list the details of overlaps between H3K27me3 and H3K4me3 in each anatomical region, as well as overlaps for each of the histone markers across anatomical regions.</li> </ul> </li> </ul>
Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
<p>Datasets that contain a minimum of nanopore reads sufficient for hidden Markov model training and for evaluating the performance of our computational tool - nanoHiMe at simultaneously calling CpG and/or adenine methylation on individual nanopore reads.<em> Ecoli</em>_PCR_amplicons_100k.tgz, <em>Ecoli</em>_PCR_MSssI_100k.tar.gz and <em>Ecoli</em>_PCR_pA-Hia5_100k.tar.gz are used for training new parameters of the emission distributions of individual <em>k</em>-mers from DNA template without modification, with fully methylated CpGs, and with partially methylated adenines, respectively. nanoHiMe_H3K27me3.fast5.tgz are the nanopore sequencing reads from H3K27me3 nanoHiMe-seq experiments in GM12878 cells and used for evaluating the performance of nanoHiMe at jointly calling CpG and adenine methylation.</p>
STORM Data: Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters
<p>The dataset underlying the SMLM STORM super-resolution images of 'Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters'. See Biorxiv paper for details on sample preparation: <a href="https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf">https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf</a>, Pyranose Oxidase STORM buffer on Elyra 7 Zeiss Microscope, processed with Zen Black. Samples are named according to which figures they occur in the above paper.</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>
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>
Histone H1 variants in Arabidopsis are subject to numerous post-translational modifications, both conserved and previously unknown in histones, suggesting complex functions of H1 in plants - raw data
<p>Data from HPLC coupled with mass spectrometer acquired during experiments.<br /> </p>
Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations
<p>Supplementary data of manuscript <strong>'Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations </strong><strong>Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations'</strong></p>
Dataset: lhp1 FLC-Venus time course imaging – Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory
<p>The histone modification H3K27me3 plays a central role in Polycomb-mediated epigenetic silencing. H3K27me3 recruits and allosterically activates Polycomb Repressive Complex 2 (PRC2), which adds this modification to nearby histones, providing a read/write mechanism for inheritance through DNA replication. However, for some PRC2 targets, a purely histone-based system for epigenetic inheritance may be insufficient. We address this issue at the Polycomb target Flowering Locus C (FLC) in Arabidopsis thaliana, as a narrow nucleation region of only ~three nucleosomes within FLC mediates epigenetic state switching and subsequent memory over many cell cycles. To explain the memory's unexpected persistence, we introduce a mathematical model incorporating extra protein memory storage elements with positive feedback that persist at the locus through DNA replication, in addition to histone modifications. Our hybrid model explains many features of epigenetic switching/memory at FLC and encapsulates generic mechanisms that may be widely applicable.</p>
Effect of Exercise Gene Expression and Histone Modifications in Patients With Hemiplegia
ClinicalTrials.gov study NCT06726941. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Dataset: lhp1 FLC-Venus time course imaging – Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory
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Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual bovine blastocysts by NTU-CAT
<p>BAM and corresponding BW files generated by NON-TiE-UP CUT&Tag (NTU-CAT).</p>
Raw Data of Inhibition of Neddylation Disturbs Zygotic Genome Activation Through Histone Modification Change and Leads to Early Development Arrest in Mouse Embryos
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Data for "A benchmark of computational pipelines for single-cell histone modification data"
<p>The `time_features.txt` and `time_correct.txt` files contain the runtimes for the various embedding methods.</p> <p>The .csv files contain the computed scores (both supervised and unsupervised) for all the methods.</p>
Resetting epigenetic memory by reprogramming of histone modifications in mammals
GEO Series GSE76687. Mus musculus. 27 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Global mapping of estrogen receptor and histone modifications in breast tumor samples uncovers distinct patterns for aromatase inhibitor resistance
GEO Series GSE40867. Homo sapiens. 36 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dynamic regulation of histone modifications and long-range chromosomal interactions during post-mitotic transcriptional reactivation
GEO Series GSE141139. Homo sapiens. 114 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Genome-wide shifts in histone modification patterns at early stage of rice infection with root-knot nematode Meloidogyne graminicola
GEO Series GSE152783. Oryza sativa Japonica Group. 6 samples. Type: Expression profiling by high throughput sequencing.
Rapid clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation: ChIP-chip
GEO Series GSE19447. Mus musculus. 27 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Genome-wide analysis of histone modifications in human endometrial stromal cells [ChIP-Seq]
GEO Series GSE57007. Homo sapiens. 20 samples. Type: Genome binding/occupancy 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.