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293 results for “Phase Separation”
Data for: Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis
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Reconstitution of phase-separated signaling clusters and actin polymerization on supported lipid bilayers
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DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic function
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EUREC4A: HALO flight phase separation: Awesome Albatross
<p>Awesome Albatross is the first version of the flight segmentation for HALO flights during the EUREC4A field campaign.</p>
Data from: Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock
<p>Circadian clocks are composed of molecular oscillators that pace rhythms of gene expression to the diurnal cycle. Therein, transcriptional-translational negative feedback loops (TTFLs) generate oscillating levels of transcriptional repressor proteins that regulate their own gene expression. In the filamentous fungus Neurospora crassa, the proteins Frequency (FRQ), the FRQ-interacting RNA helicase (FRH) and Casein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the White-Collar complex (WCC). A key question concerns how FRQ orchestrates molecular interactions at the core of the clock despite containing little predicted tertiary structure. We present the reconstitution and biophysical characterization of FRQ and the FFC in unphosphorylated and highly phosphorylated states. Site-specific spin labeling and pulse-dipolar ESR spectroscopy provides domain-specific structural details on the full-length, 989-residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging of Neurospora hyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino-acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic circadian clocks. </p>
Dataset from: Sequence grammar underlying unfolding and phase separation of globular proteins
<p>Dataset related to the figures from the paper "Sequence grammar underlying unfolding and phase separation of globular proteins". The raw mass spectrometry proteomics data have been deposited via the PRIDE partner repository to the ProteomeXchange Consortium under the dataset identifier PXD033716. </p>
Data for Taylor Dispersion-Induced Phase Separation for the Efficient Characterisation of Protein Condensate Formation
<p>This archive contains data files the Python 3 code needed to reproduce the analysis done for the publication "Taylor Dispersion-Induced Phase Separation for the Efficient Characterisation of Protein Condensate Formation". Most of the data files are recorded on the Fida 1 instrument (Fidabio, Denmark) and consists of fluorescence recordings at the end of a 1 m long microfluidic channel (Ø 75 µm). Additional data file types include raw microscopy images (Leica SP8 confocal microscope, Germany), spectroscopy and light scattering files from Probedrum/Labbot (Labbot, Sweden), and simulation files generated by Comsol 6 (COMSOL AB, Sweden). Comsol project files are also supplied.</p> <p>The Python code is supplied in the form of Jupyter Notebooks. A python file "TDIPS.py" contains general routines used in the data analysis notebooks, and is for example capable of calculating the viscosity of various salt solution mixtures using table values. This is used for normalisation of the Fida 1 instrument data, when several measurements are done at different salt concentrations.</p> <p>The scripts are running Python 3.11.7 and packages Numpy (1.26.4), Matplotlib (3.8.0), Pandas (2.1.4), Scipy (1.11.4), and LMfit (1.2.2).</p> <p>All figures are included as Scalable Vector Graphics (<em>SVG</em>) files and can be opened using Inkscape.</p> <p>© Technical University of Denmark</p>
Single particle tracking data for "Histidine-rich domain of kinases induce phase separation to hyperphosphorylate Pol II CTD"
<p><strong>Experimental single-particle tracking (SPT) data supporting "Histidine-rich domain of kinases induce phase separation to hyperphosphorylate Pol II CTD"</strong></p> <p>This dataset contains all the raw SPT data reported in "Histidine-rich domain of kinases induce phase separation to hyperphosphorylate Pol II CTD" in the form of SPT trajectories. The SPT trajectories are provided in two different formats for convenience: a CSV format and a Matlab format. Both formats are readable by Spot-On: https://spoton.berkeley.edu/</p> <p>The SPT data contains "fast tracking" spaSPT data (Figure 2d) and this data was analyzed using the Matlab version of Spot-On which can be found and downloaded at: https://gitlab.com/tjian-darzacq-lab/spot-on-matlab</p> <p>The SPT data also contains "slow tracking" SPT data (Figure 2e).</p> <p>Full details about the Matlab and CSV formats are provided in the ReadMe files in the associated zip files.</p> <p>Please see the associated manuscript for a detailed description of how the data was acquired and analyzed. For questions about the data please contact Anders Sejr Hansen at anders.sejr.hansen {at} berkeley {dot} edu.</p>
Chromocenter image processing and data for "Volume buffering in multi-component phase separation"
<p>Contains image processing code and a csv of the image processing results for the images of chromocenters in mammalian cells for the paper "Volume buffering in multi-component phase separation".</p>
Dataset for Periodic phase-separation during meniscus-guided deposition
<p>Partial dataset for the publication: Periodic phase-separation during meniscus-guided deposition, authored by R. de Bruijn, A.A. Darhuber, J.J. Michels, P. van der Schoot.</p> <p>The data files contain the relevant volume fraction fields for Figures 6 and 10 of this publication.</p>
PhasAGE Training School 1 - Phase separation and emergent functions of Intrinsically Disordered Proteins- Lecture
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
An alternative cytoplasmic SFPQ isoform with reduced phase separation potential is upregulated in ALS
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Data from: Engineering a spatiotemporal macrophage circuit via STING phase separation to override immune suppression in pancreatic cancer
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Data from: Multi-scale structure of chromatin condensates explains phase separation and material properties
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Data from: Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock
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Dynamics of phase separation of sheared inertialess binary mixtures
<p>Videos (gif files) of the simulated dynamics of phase separation report the maps of mass fraction of species <em>A</em> (<em>f</em>) at different time intervals within the simulated domain. File names are as follows:</p> <p>Sec3.<strong>s</strong>_gamma<strong>G</strong>_Nalpha<strong>N</strong>_MC<strong>n</strong>_tstep<strong>T</strong>-phi</p> <p>where:</p> <p><strong>s</strong> identifies the section number as in the main text (i.e., Sec3.1, Sec3.2, Sec3.3, Sec3.4)</p> <p><strong>G</strong> identifies the value of the dimensionless shear rate (e.g., 0, 10<sup>-2</sup>, etc.)</p> <p><strong>N</strong> identifies the value of the fluidity parameter <em>N</em><em><sub>a</sub></em> (e.g., 10<sup>-2</sup>, 10<sup>2</sup>, etc.)</p> <p><strong>n</strong> identifies the different realizations of the initial random noise (i.e., MC1, MC2)</p> <p><strong>T</strong> identifies the time step in dimensionless time (i.e., tstep20, tstep200)</p>
Binary 2D morphologies of polymer phase separation
<p>This dataset was generated through the simulation of a time evolving Cahn -Hilliard equation, describing phase separation in binary polymer blends. Several realizations of the equation were done through different values of volume fractions and binary interaction parameters. Morphologies were outputted at constant time intervals. Fill factor information for each instance has been provided as well.</p> <p> </p>
Data files for the publication "Surfactants Regulate the Mixing State of Organic-Inorganic Mixed Aerosols Undergoing Liquid-Liquid Phase Separation"
<p>Data files for the publication “Surfactants Regulate the Mixing State of Organic-Inorganic Mixed Aerosols Undergoing Liquid-Liquid Phase Separation”</p>
Supplementary materials used for the research to predict phase separation in protein chains
<p>This is a collection of all the data, codes and metadata that were used for the research titled: 'Sequence based prediction of protein phase separation into disordered condensates using machine learning'.</p>
Phase separation of competing memories along the human hippocampal theta rhythm.
<p>Data set for Phase separation of competing memories along the human hippocampal theta rhythm.</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.