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Dataset results
219 results for “phd”
Clinical Status Monitoring in Implantable Cardiac Defibrillator (ICD) Patients by Physiological Diagnosis (PhD) Function
ClinicalTrials.gov study NCT01170624. IPD Sharing: Not stated. Countries: 5. Publications: 0.
Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling [single-cell RNA-seq]
GEO Series GSE150089. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression
GEO Series GSE30478. Homo sapiens. 3 samples. Type: Expression profiling by array.
The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis [ChIP-seq]
GEO Series GSE205109. Arabidopsis thaliana. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Separable functions of the PHD finger protein Spp1 in the Set1 and the meiotic DSB forming complexes cooperate for meiotic DSB formation
GEO Series GSE102790. Saccharomyces cerevisiae. 3 samples. Type: Genome binding/occupancy profiling by array.
Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a [gene expression]
GEO Series GSE73446. Mus musculus. 9 samples. Type: Expression profiling by array.
Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a
GEO Series GSE63974. Mus musculus. 95 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
Role of Yng2 PHD and CHD-containing Eaf3 subunits of NuA4 on genome wide histone H4K8 acetylation, NuA4 localization and Pol II distribution
GEO Series GSE77945. Saccharomyces cerevisiae. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes [ChIP-Seq]
GEO Series GSE221659. Arabidopsis thaliana. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling
GEO Series GSE150090. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes
GEO Series GSE221660. Arabidopsis thaliana. 23 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
PhD Thesis: Tracing Molecular Patterns of Adaptation in Arctic Brassicaceae
<p>Extreme environments can function as natural laboratories for studying how different organisms adapt to similar selection pressures at the genetic level. This thesis explores how three Arctic plant species independently adapted to some of the coldest biomes on Earth, and how they evolved similar suites of adaptations to extremes in light and temperature. It addresses fundamental questions in plant evolutionary biology, such as the extent to which adaptation follows the same genetic trajectories in different species, and the genetic basis for plant adaptation to extreme environments. The thesis has <u>two main objectives</u> that are addressed through three papers (<b>Papers I-III</b>):<b> </b>1) estimate the degree of adaptive molecular convergence in the three Arctic Brassicaceae <i>Cardamine bellidifolia</i>, <i>Cochlearia groenlandica</i>, and <i>Draba nivalis</i>, and 2) identify putative molecular adaptations to the Arctic environment in the same three species.</p> <p><b>Approach. </b>The first two papers examine the degree of evolutionary repeatability in how <i>C. bellidifolia</i>, <i>C. groenlandica</i>, and <i>D. nivalis</i> adapted to the Arctic environment at the genetic level (<u>objective 1</u>). In <b>Paper I</b>, we estimated molecular convergence at the level of codons, genes, and functional pathways, by comparing genome-wide patterns of positive selection and identifying convergent substitutions in the three species. In <b>Paper II</b>, we conducted a time series experiment to examine the transcriptional responses of the Arctic Brassicaceae to low temperatures, and to identify potential convergent expression patterns in cold response.</p> <p>All three papers identify putative molecular adaptations to extremes in light and temperature (<u>objective 2</u>). In <b>Paper I</b>, we identified candidate genes for adaptation to the Arctic environment by searching for positively selected genes associated with abiotic stresses common in the Arctic. In <b>Paper II</b>, we explored the molecular basis of cold tolerance in Arctic Brassicaceae, and described how their cold-induced transcriptomes differ from that of the temperate model species, <i>Arabidopsis thaliana</i>. In <b>Paper III</b>, we assembled the genome of <i>D. nivalis</i> and explored the genomic characteristics of Arctic plant adaptation, by conducting comparative analyses of chromosomal evolution and functional genomics with other species in the Brassicaceae.</p> <p><b>Main findings and discussion. </b>The findings in <b>Papers I-II</b> suggests that the three Arctic Brassicaceae have adapted to the Arctic environment through independent genetic trajectories (<u>objective 1</u>). In <b>Paper I</b>, we found that positive selection has been acting on different genes, but similar functional pathways in the three species. The positively selected genes sets showed convergent functional profiles associated with abiotic stresses common in the Arctic. However, we found little evidence for convergent substitutions at the same sites, or for positive selection acting on the same genes in the three species. In <b>Paper II</b>, we found that the cold-response of <i>C. bellidifolia</i>, <i>C. groenlandica</i>, and <i>D. nivalis</i> was highly species-specific. Most cold-induced genes were unique for each species, and the number of genes shared by the three Arctic species and the temperate <i>A. thaliana</i> was higher than the number of genes shared by the Arctic species alone. This suggests that the cold response in Arctic Brassicaceae mainly evolved independently, but with some components likely conserved across the family. The low levels of molecular convergence could be explained by the many evolutionary trajectories leading to better performance under temperature and light stress in plants, and/or less repeatable patterns of adaptation in highly polygenic traits such as cold tolerance.</p> <p><b>Papers I-III</b> presents some of the first molecular evidence for putative plant adaptations to the Arctic environment (<u>objective 2</u>). In <b>Paper I</b>, we found multiple candidate genes for Arctic adaptation associated with cold stress, freezing stress, oxidative stress and light stress in all species. Adaptations associated with the plasma membrane seemed to be particularly important in all species, possibly due to its crucial role in freezing tolerance. In <b>Paper II</b>, we found that the Arctic cold response followed similar trends as in the temperate <i>A. thaliana</i>, but a few genes and characteristics were specific for the Arctic species alone. In <b>Paper III</b>, we presented a 302 Mb assembly of <i>D. nivalis</i> that is highly contiguous with 91.6 % assembled into eight chromosomes (the base chromosome of the species). We found that the <i>D. nivalis</i> genome contains expanded suites of genes associated with common Arctic stresses, and the expansion of these gene families appear to partly be driven by the activity of transposable elements.</p> <p><b>Conclusion. </b>The results from this dissertation provide a framework for studies that aim to test the existence of a functional syndrome of Arctic adaptation in Brassicaceae and other flowering plants. The <i>D. nivalis</i> genome assembly may also become an important tool in studies of Arctic plant evolution in general. </p>
Fungomeli_Maria_PhD_Thesis_Appendices_Dec_2020
<p>Vegetation Data set used as Appendices in the PhD Thesis, December 2020.</p>
Supplementary_table_PhD_LisonZunino_Article3
Open the record for dataset details and reuse information.
Materials for the PhD Thesis "Gender-Fair Language in Translation and Post-Editing: Insights and Best Practices"
<div> <div> <div> <p>These materials include:</p> <ul> <li> <p>Call for participation in the study.</p> </li> <li> <p>Document containing information about the study procedure.</p> </li> <li> <p>Informed consent form.</p> </li> <li> <p>Handout on gender­fair language.</p> </li> <li> <p>Three text assignments for translation and post­editing.</p> </li> <li> <p>Interview guides.</p> </li> <li> <p>Interview transcriptions.</p> </li> <li> <p>MAXQDA project file containing the codes for the interview analysis.</p> </li> <li> <p>Target text annotations.</p> </li> <li> <p>Observational protocols.</p> </li> <li> <p>Excel sheet providing an overview of the process data.</p> </li> </ul> </div> </div> </div>
Simulation data on ORF6 from SARS-CoV-2 for a PhD thesis submitted to University College London
<p><strong>Unpublished data from a thesis submitted to University College London in September 2024 </strong></p> <p><em>Thesis title: Biophysical characterisation of ORF6 from SARS-CoV-2</em></p> <p><em><strong>Chapter 5 - full-length ORF6 metadynamic simulations in the AMBER03ws force field </strong></em></p> <p>The `Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz` directory contains data for a 61-residue disordered protein. The protein is ORF6 from SARS-CoV-2. The data were produced by metadynamics simulations in the AMBER03ws force field. I used PLUMED version 2.7.1 and GROMCS 2021.2. All the data and PLUMED input files required to reproduce the simulation results are available on PLUMED-NEST. This data should be used with the code provided on GitHub at [`https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/full-length_orf6`](https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/full-length_orf6)</p> <p>Once downloaded, this directory should be extracted using the following command: </p> <p>tar -xzvf Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz</p> <p>The directory should be saved with the name `Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz`` and placed in the same directory as the GitHub `README_metadynamic_simulations.md` file. </p> <p><strong>This dataset contains: </strong></p> <ul> <li> .pdb - atomic coordinate files for full-length ORF6 in the a03ws force field.</li> <li>_traj.trr - single concatenated trajectory files for the a03ws (ctr is just the last 21 residues of the full-length simulation).</li> <li>_weights_corr.dat - weights for each frame in _traj.trr for the a03ws run. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 1.2 nm.</li> <li>top_frames_.npy - numpy array of frames index for the a03ws simulations. Frames were selected based on weights_corr.dat.</li> <li>top_frames_.trr - trajectory of frames for the a03ws. Frames were selected based on weights_corr.dat</li> <li>CS_COLVAR_{system} - experimental and CamShift predicted chemical shifts for the last 21-residues of the full-length ORF6 simulation. </li> <li>Contacts directory: Contains Coulomb and LJ input files to make the contact maps. </li> </ul> <p><em><strong>Chapter 5 - ORF6-RAE1-NUP98_GLEBS metadynamic simulations in the AMBER99SB-disp force field </strong></em></p> <p>The `Metadynamic_ORF6_complex_simulations_Zenodo.tar.xz` directory contains data for the RAE1-NUP98-ORF6 complex. This was built upon the crystal structure: [`https://www.rcsb.org/structure/7VPH`](https://www.rcsb.org/structure/7VPH). The data were produced by metadynamics simulations in the AMBER99SB-disp force field. I used PLUMED version 2.7.1 and GROMCS 2021.2. This data should be used with the code provided on GitHub at [`https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/orf6-rae1-nup98`](https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/orf6-rae1-nup98)</p> <p>Once downloaded, this directory should be extracted using the following command: </p> <p>tar -xzvf Metadynamic_ORF6_complex_simulations_Zenodo.tar.xz</p> <p><strong>This dataset contains: </strong></p> <ul> <li>.pdb - atomic coordinate files for the complex in the AMBER99SB-disp force field</li> <li>traj.trr - single concatenated trajectory files for the</li> <li>_weights_corr.dat - weights for each frame in _traj.trr for the AMBER99SB-disp force field. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 1.2 nm. weights.dat is before this process.</li> <li>COLVAR files </li> </ul> <p>128 starting conformations (gro) files for each system listed above. </p>
PhD_Thesis_Aline_Carrel_NMR_Data
<p>NMR Data for the PhD Thesis "Exploring Bicyclic Diamines as Drug Scaffolds"</p>
The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis
GEO Series GSE205112. Arabidopsis thaliana. 30 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
PhD Thesis: Tracing Molecular Patterns of Adaptation in Arctic Brassicaceae
Open the record for dataset details and reuse information.
Global transcriptional changes upon Bromodomain (BrD) deletion in PfGCN5 and PHD domain deletion in PfPHD1 by transcriptome analyses via RNA-seq
GEO Series GSE164070. Plasmodium falciparum. 36 samples. Type: Expression 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.