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382 results for “chromatin structure”
Suppl. Information to "The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching"
<p><strong>Supplementary File 1:</strong> Multiple alignment for protein sequences of core histones with Pocillopora acuta, Pocillopora damicornis, Acropora digitifera, Nematostella vectensis, Hydra vulgaris, Schistosoma mansoni and Mus musculus. A. Histone H2A; B. Histone H2B; C. Histone H3; D. Histone H4. An asterisk (*) means that the amino acid is conserved between all species.</p> <p><strong>Supplementary File 2</strong>: Original (uncropped and unedited) images used for Figures 1 to 4.</p> <p><strong>Supplementary File 3:</strong> <em>P. acuta</em> nuclei and <em>Symbiodinium</em> count on a Thoma cell counting chamber done over three different nuclei extractions. For each extraction, two counts were performed. P. acuta nuclei were stained with Hoechst 33342 and display a blue fluorescence at 350 nm. Symbiodinium are not damaged by our extraction method and are not permeable to Hoechst. They display a red fluorescence because of their chlorophyl content. Observations were done on a Leica DMLB with objective PL Fluotar 40x and 100x. A text version of the data in the Excel file below.</p> <p>Extraction #1 replicate 1: 102 <em>P. acuta</em> nuclei (Blue) ; 2 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 112 <em>P. acuta</em> nuclei (Blue) ; 2 <em>Symbiodinium</em> (Red)</p> <p>Extraction #1 replicate 1: 42 <em>P. acuta </em>nuclei (Blue) ; 0 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 55 <em>P. acuta </em>nuclei (Blue) ; 1 <em>Symbiodinium</em> (Red)</p> <p>Extraction #1 replicate 1: 215 <em>P. acuta </em>nuclei (Blue) ; 3 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 257 <em>P. acuta</em> nuclei (Blue) ; 5 <em>Symbiodinium</em> (Red)</p> <p>Made at IHPE.</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4e
<p>The single-molecule FRET dataset underlying Fig. 4e of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4f
<p>The single-molecule FRET dataset underlying Fig. 4f of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4d
<p>The single-molecule FRET dataset underlying Fig. 4d of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
<p>This upload contains the FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.</p> <p>If you use the datasets, we would be grateful if you cited the following paper:</p> <p>Zou, C., Zhang, Y., Ouyang, Z. (2016) HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biology, 17: 40.</p>
Application of flow cytometry using advanced chromatin analyses for assessing changes in the sperm structure and DNA integrity in a porcine model
<p><span>Chromatin status is critical for sperm fertility. We tested a multivariate approach for studying pig sperm chromatin, aiming to capture the chromatin structure's complexity with a set of quick and simple techniques, not only DNA damage. Sperm doses from 36 boars (3 ejaculates/boar) were analyzed at days 0 and 11 (cooled storage). Analyses were: CASA (motility) and flow cytometry to assess sperm functionality and chromatin structure by SCSA (DNA fragmentation %DFI and chromatin maturity %HDS), monobromobimane (mBBr, tiol status/disulfide bridges between protamines), chromomycin A3 (CMA3, protamination) and 8-hydroxy-2'-deoxyguanosine (8-oxo-dG, DNA oxidative damage). Data were analyzed by linear models for effects of boar and storage, correlations, and multivariate analysis as hierarchical clustering and principal component analysis (PCA). Storage reduced sperm quality parameters, mainly motility, with no critical oxidative stress increases, while chromatin status worsened slightly (%DFI and 8-oxo-dG increased while mBBr MFI and disulfide bridges decreased). Boar significantly affected most chromatin variables except for CMA3, with storage affecting most except %HDS. At day 0, sperm chromatin variables clustered closely, except for CMA3, and %HDS and 8-oxo-dG correlated with many variables (notably, mBBr). After storage, the relation between %HDS and 8-oxo-dG remained, but correlations among other techniques disappeared, and mBBr variables clustered separately. The PCA suggested a considerable influence of mBBr on sample variance, especially regarding storage, with SCSA and 8-oxo-dG affecting between-sample variability. Overall, CMA3 was the least informative, in contrast with results in other species. The combination of DNA fragmentation, DNA oxidation, chromatin compaction, and tiol status seems a good candidate for obtaining a complete picture of the pig sperm nucleus status, raising many questions for future molecular studies and deserving further research to establish its usefulness as fertility predictors in multivariate models. The meaning of CMA3 should be clarified.</span></p>
Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements
<p>Structural variant calls, RepeatMasker annotations, and genome assemblies of diverse mouse genomes. </p>
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
<p>ncVarPred-1D3D:</p> <p>The data used for testing the inconsistency among genome sequence, epigenetic profile, and later, to show its relation to 3D chromatin structure can be found in sanity_check_data.tar.gz.</p> <p>Some trained model for noncoding mutation effect prediction (mapping genome sequence to epigenetic profile) can be found in CNN_MLP, CNN_GCN, CNN_RNN_MLP, CNN_RNN_GCN.tar.gz.</p> <p>The trained model for pathogenic variants prediction can be found in fewshot_pathogenic_model.tar.gz. </p> <p>The training data can be found in training_data.tar.gz.</p> <p>Some noncoding variant effects prediction results, e.g. eQTL and pathogenic variants, can be replicated using the data shared in ncVar_data.tar.gz.</p>
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
<p>ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed.</p> <p>The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.</p>
Data from: Multi-scale structure of chromatin condensates explains phase separation and material properties
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3D chromatin structures associated with ncRNA roX2 for hyperactivation and co-activation across the entire X chromosome
<p>The SMLM datasets of roX2 and roX2/H3K27me3.</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.
Altered 3D chromatin structure permits inversional recombination at the IgH locus
<p>Immunoglobulin heavy chain (<i>IgH</i>) genes are assembled by two sequential DNA rearrangement events that are initiated by recombinase activating gene products (RAG) 1 and 2. Diversity gene segments (D<sub>H</sub>) rearrange first, followed by variable (V<sub>H</sub>) gene rearrangements. Here we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. D<sub>H</sub> gene segments, that recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on WT <i>IgH</i> alleles, V<sub>H</sub> and D<sub>H</sub> gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that V<sub>H</sub> gene segments find their targets by diffusion-controlled mechanisms. These distinct mechanisms may underlie differential allelic choice associated with each step of <i>IgH</i> gene assembly.</p>
Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription
<p>Dataset required for running leukemia associated structural variants scoring described in Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription manuscript.</p>
Fat distribution in women associates with depot-specific transcriptomics signatures and chromatin structure
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Altered 3D chromatin structure permits inversional recombination at the IgH locus
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Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
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Open Chromatin structure
SciDraw upload
Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus
GEO Series GSE74709. Homo sapiens. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [II]
GEO Series GSE190136. Saccharomyces cerevisiae. 29 samples. Type: Other.
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.