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821 results for “epigenetic regulation”
Genetic and epigenetic regulation of zebrafish intestinal development
<p>This dataset contains zebrafish (<em>Danio rerio</em>) raw RNA and ChIP (paired-end) sequencing data:</p> <ul> <li>RNA-seq <ul> <li>lane1_BSwt5dpf*: 3 biological replicates of RNA-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt7dpf*: 3 biological replicates of RNA-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt9dpf*: 3 biological replicates of RNA-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> <li>ChIP-seq <ul> <li>Cldn-wt-int-5dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> </ul>
Supplemental Data to PhD Dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering"
<p>Supplemental Data to the PhD dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering" from Suze Blom, Wageningen University & Research (doi:10.18174/670822). Supplementary data to the chapter entitled "Ambient temperature dependent changes in DNA methylation in Arabidopsis thaliana Col-0 and the decrease in DNA methylation 1 mutant" [manuscript in preparation]</p> <p>Includes Supplemental Data:</p> <p>Supplementary Data 1: Significantly differently expressed (DE) genes in Col-0 after the 24 hour ambient temperature switch from 16°C to 25°C. padj value of 0.05 was set as the cutoff value for statistical significance.</p> <p>Supplementary Data 2: Significantly differently expressed (DE) genes in ddm1-10 after the 24 hour ambient temperature switch from 16°C to 25°C. padj value of 0.05 was set as the cutoff value for statistical significance.</p> <p>Supplementary Data 3: Alternative splicing (AS) of transcripts after an ambient temperature change from 16°C to 25°C in Col-0. Gene ID, splicing event, genomic location, AS frequency and padj values are indicated.</p> <p>Supplementary Data 4: Alternative splicing (AS) of transcripts after an ambient temperature change from 16°C to 25°C in ddm1-10. Gene ID, splicing event, genomic location, AS frequency and padj values are indicated.</p> <p>Supplementary Data 5: List of genes in Col-0 (sheet 1) and ddm1-10 (sheet 2) with both significant AS and DMC associated with them. Gene ID and number of DMCs associated with the gene are indicated.</p>
Dataset for Article - a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle
<p>This dataset contains data for analysis on a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle. Dataset contains raw gene expression data, methylation-ELISA data, MSRE data and life history data collected in laboratory conditions using the study system, <em>Callosobruchus maculatus</em>.</p>
Inducible TDG knockout models to study epigenetic regulation
<p>Mechanistic and functional studies by gene disruption or editing approaches often suffer from confounding effects like compensatory cellular adaptations generated by clonal selection. These issues become particularly relevant when studying factors directly involved in genetic or epigenetic maintenance. To provide a genetic tool for functional and mechanistic investigation of DNA repair mediated active DNA demethylation, we generated a <em>Tdg </em>minigene model in mice and mouse embryonic stem cells (ESCs). The floxed <em>miniTdg</em> is rapidly and reliably excised by tamoxifen-induced Cre expression in mice and ESCs, depleting TDG to undetectable levels within 24 hours of induction. We describe the functionality of the engineered <em>miniTdg</em> in mouse and ESCs (TDGiKO ESCs) and validate the pluripotency and differentiation potential of TDGiKO ESCs as well as the phenotype of induced TDG depletion. The controlled and rapid depletion of TDG allows for a precise manipulation at any time point in multistep experimental procedures as presented here for neuronal differentiation <em>in vitro</em>. Thus, we provide a thoroughly validate d genetic tool for the functional and mechanistic investigation of TDG in active DNA (de)methylation and/or DNA repair with minimal interference from adaptive effects and clonal selection.</p>
A systems biology approach to identify essential epigenetic regulators for specific biological processes in plants
<p>Supplemental Files for McCoy et al "A systems biology approach to identify essential epigenetic regulators for specific biological processes in plants"</p>
Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae
<p>Datasets for the code analysis in <em>Priego-Cubero, Knoch et al., 2024 </em>(https://doi.org/10.1101/2024.10.02.615186)</p>
Epigenetic Regulation in Fibrous Dysplasia of Bone: mirDYS Study.
ClinicalTrials.gov study NCT03838991. IPD Sharing: NO. Countries: 1. Publications: 1.
A Case Control Study to Identify the Role of Epigenetic Regulation of Genes Responsible for Energy Metabolism and Mitochondrial Function in the Obesity Paradox in Cardiac Surgery
ClinicalTrials.gov study NCT02908009. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Epigenetic Regulation of Immunity in Alpha-1 Anti-trypsin Deficiency
ClinicalTrials.gov study NCT02691611. IPD Sharing: NO. Countries: 1. Publications: 33.
Epigenetic Regulation of Human Adipose Tissue Distribution
ClinicalTrials.gov study NCT02728635. IPD Sharing: NO. Countries: 1. Publications: 38.
Epigenetic Analysis of Regulation of the Inflammasome-activating NLRP3 Gene in Monocytes From Atrial Fibrillation Patients and Controls
ClinicalTrials.gov study NCT04766814. IPD Sharing: Not stated. Countries: 1. Publications: 25.
Epigenetic Regulation of Exercise Induced Asthma
ClinicalTrials.gov study NCT05174689. IPD Sharing: NO. Countries: 1. Publications: 27.
Epigenetic Regulation of Osteogenesis Imperfecta Severity : miROI Study
ClinicalTrials.gov study NCT04009733. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: DNA methylation and potential for epigenetic regulation in Pygospio elegans
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Data from: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics
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Raw data related to: Molecular Mechanisms Controlling Foxp3 Expression in Health and Autoimmunity: From Epigenetic to Post-translational Regulation.
<p><strong>Abstract</strong></p> <p>The discovery of the transcription factor Forkhead box-p3 (Foxp3) has shed fundamental insights into the understanding of the molecular determinants leading to generation and maintenance of T regulatory (Treg) cells, a cell population with a key immunoregulatory role. Work over the past few years has shown that fine-tuned transcriptional and epigenetic events are required to ensure stable expression of Foxp3 in Treg cells. The equilibrium between phenotypic plasticity and stability of Treg cells is controlled at the molecular level by networks of transcription factors that bind regulatory sequences, such as enhancers and promoters, to regulate Foxp3 expression. Recent reports have suggested that specific modifications of DNA and histones are required for the establishment of the chromatin structure in conventional CD4+ T (Tconv) cells for their future differentiation into the Treg cell lineage. In this review, we discuss the molecular events that control Foxp3 gene expression and address the associated alterations observed in human diseases. Also, we explore how Foxp3 influences the gene expression programs in Treg cells and how unique properties of Treg cell subsets are defined by other transcription factors.</p> <p> </p> <p><strong>Progetto giovani ricercatori</strong>[GR-2016-02363725] dal titolo: "Immune Tolerance, Metabolism and Multiple Sclerosis: Novel Molecular Tools to Monitor Disease Pathogenesis and Progression"</p> <p> </p> <p> </p> <p> </p>
Transcriptomic analysis and epigenetic regulators in human oocytes at different stages of oocyte meiotic maturation
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Epigenetic regulation of autonomous pathway mediates polymorphism of flowering time in Arabidopsis
<p><span>Plant flowering time is affected by endogenous and exogenous factors, but its polymorphism among different populations of a species has not been fully explained yet. Here, 27 <em>Arabidopsis thaliana</em> populations were used to </span><span>determine</span><span> how autonomous pathway gene methylation affects flowering differences </span><span>by</span><span> regulating gene expression patterns. DNA methylation analysis, qPCR and transgenic verification</span> <span>showed that polymorphism in the flowering time among the <em>Arabidopsis</em> populations ranged from 19 to 55 days was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway</span><span>,</span><span> <em>FVE</em>, <em>FY</em>, <em>FLD</em>, <em>PEP</em>, <em>HDA5</em> and <em>PPR</em> <em>39-1</em> and</span><span> their </span><span>relative expression levels</span> <span>(P < 0.05). Expression of selected <em>FVE</em> and <em>FVE(CS) </em>separately</span> <span>through codon degeneracy substitution of cytosine led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of </span><span>methylated sites</span><span> of <em>FVE</em> and <em>FVE(CS)</em> among those transgenic plants and recipient Col-0 verified the close relationship between their methylation number, expression and the flowering times. Our findings firstly suggest that the methylation variation of those six key upstream transcription factors regulates</span><span> the</span><span> gene expression level of </span><span>the</span><span> autonomous pathway, leading to phenotypic differences in flowering time of Arabidopsis. </span><span>The</span><span> <em>FVE(CS)</em></span><span> and <em>FVE</em> genes in transgenic plants tend to be hypermethylated, and this could be a protective mechanism for plants. However, modification of gene sequence through codon degeneracy substitution to reduce cytosine can avoid hypermethylated transferred-genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology.</span></p>
Supplemental Data to PhD Dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering"
<p>Supplemental Data to the PhD dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering" from Suze Blom, Wageningen University & Research (doi:10.18174/670822). Supplemental data to the Chapter: "Characterisation of multiple novel lncRNAs involved in ambient temperature sensitive flowering in Arabidopsis thaliana" [manuscript in preparation].</p> <p>Includes Supplemental Data:</p> <p><strong><span>Supplementary Data 1: </span></strong><span>Analysis of publicly available ChIP-seq datasets to test whether a selection of TFs binds in proximity to genomic lncRNA sites. Sheet 1: TF list and GSE numbers. Sheet 2: TF ChIP-seq peak annotation, signal, and direction found in proximity to lncRNA genomic loci.</span></p> <p> </p>
BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III
<p>This is a high content drug screening dataset composed of images and single-cell analysis results from a 384-well plate </p> <p>The SPLICS reporter is composed of a split GFP1-10 barrel localized to the mitochondrial outer membrane, a P2A self-cleavage signal for equimolar expression, and the remaining beta11 fragment targeted to the ER membrane. Upon ERMCS formation within the 8-10 nm distance, the split-GFP reporter forms intact GFP. Doxycycline-inducible SPLICS reporter stable cell lines were generated via a three-plasmid PiggyBac transposase system. Cells were co-transfected with the plasmids using Lipofectamine 2000 transfection reagent, then the next day selected with 2 mg/ml of G418 (Geneticin) for 7 days. With the SPLICS integrated cells, mitochondrial TagRFP is expressed in them. For mitochondrial TagRFP labeling in cells, we utilized a lentiviral backbone and introduced a mitochondria matrix TagRFP (mitoTagRFP) to control for gene expression and monitor mitochondrial abundance. After mitoTagRFP integration, 100 ng/ml of doxycycline were used to induce SPLICS reporter expression, and GFP/TagRFP double positive cells were sorted on Bigfoot Spectral Cell Sorter (Invitrogen) to isolate GFP/TagRFP positive clones. Clones were cultured and screened for accurate localization of SPLICS reporter to mitochondria and ER via live cell imaging and for normal mitochondrial oxygen consumption rate. Probe induction did not have a deleterious effect on cell number or increasing green fluorescence for at least 72 hours of reporter induction. For ERMCS analysis with SPLICS, cells will be induced with 100 ng/ml of doxycycline for minimally 24 hr before treatment or analysis.</p>
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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.