Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,004
datasets available to search
ShareScore release 0.9.0
Dataset results
1,004 results for “Cholesterol”
TRPC3 interaction with cholesterol as explored through MD (raw data)
<p>Transient receptor potential canonical 3 (TRPC3) channel belongs to the superfamily of transient receptor potential (TRP) channels which mediate Ca<sup>2+</sup> influx into the cell. These channels constitute essential elements of cellular signalling. TRPC3 is primarily gated by lipids, and its surface expression has been shown to be dependent on cholesterol, yet a comprehensive exploration of its interaction with this lipid has thus far not emerged. Here, through 80 µs of coarse-grained molecular dynamics simulations, we show that cholesterol interacts with multiple elements of the transmembrane machinery of TRPC3. Through our approach, we identify an annular binding site for cholesterol on the pre-S1 helix, and a non-annular site at the interface between the voltage-sensor like domain and pore domains. Here cholesterol interacts with exposed polar residues, and possibly acts to stabilise the domain interface.</p> <p> </p> <p><br> p { margin-bottom: 0.08in; color: #000000; line-height: 0.24in; text-align: justify; orphans: 2; widows: 2; background: transparent }p.western { font-family: "Palatino Linotype", serif; font-size: 12pt }p.cjk { font-family: "Palatino Linotype", serif; font-size: 12pt; so-language: de-DE }p.ctl { font-family: "Palatino Linotype", serif }a:visited { color: #954f72; text-decoration: underline }a:link { color: #0000ff; text-decoration: underline }</p> <p> </p>
Set simulations small pure bilayers with cholesterol (max 128 lipids) using charmm36 ff in gromacs (DPPC)
<p>Collection simulations of small pure bilayers (max 128 phospholipids) with cholesterol in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <ol> <li>DPPC_128_CHL1_32_310K</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
Supplementary Data: Evolution of the cholesterol biosynthesis pathway in animals
<p>Cholesterol plays essential roles in animal development and disease progression. Here, we characterize the evolutionary pattern of the canonical cholesterol biosynthesis pathway (CBP) in the animal kingdom using both genome-wide analyses and functional experiments. CBP genes in the basal metazoans were inherited from their last common eukaryotic ancestor and evolutionarily conserved for cholesterol biosynthesis. The genomes of both the basal metazoans and deuterostomes retain almost the full set of CBP genes, while Cnidaria and many protostomes have independently experienced multiple massive losses of CBP genes that might be due to the geologic events during the Ediacaran period, such as the appearance of an exogenous sterol supply and the frequent perturbation of ocean oxygenation. Meanwhile, the indispensable utilization processes of cholesterol potentially strengthened the maintenance of the complete set of CBP genes in vertebrates. These results strengthen both biotic and abiotic roles in the macroevolution of a biosynthesis pathway in animals.</p>
Thermal evaporation as sample preparation for silver‐assisted laser desorption/ionization mass spectrometry imaging of cholesterol in amyloid tissues
<p><strong>Thermal evaporation as sample preparation </strong><strong>for </strong><strong>silver‐assisted laser desorption/ionization mass spectrometry imaging of cholesterol in amyloid tissues</strong></p> <p>MSI datasets in SCiLS Lab SL File (*.sl) or as flexImaging sequence (*.mis)</p>
Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset
<p>The molecular dynamics (MD) simulation dataset. The contents:</p> <ul> <li><strong>5ire_BIOMT_expanded.pdb</strong>: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE) </li> <li><strong>5ire_Mprotein_BIOMT_expanded.pdb</strong>: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE). The biological assembly shows the dimeric organization of M proteins.</li> <li><strong>0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip</strong> contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively. <ul> <li>In each zip file, there are 5 directories: <strong>wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S</strong> corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files: <ul> <li><strong>toppar</strong>: This directory contains all force field topologies and parameters</li> <li><strong>topol.top</strong>: GROMACS topology (top) file</li> <li><strong>index.ndx</strong>: GROMACS index (ndx) file</li> <li><strong>prod.mdp</strong>: GROMACS MD parameters (mdp) file</li> <li><strong>0, 1, 2, 3, 4, 5, 6, 7, 8, 9</strong>: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files: <ul> <li><strong>t0.pdb</strong>: The pdb file of the starting coordinates</li> <li><strong>prod0.tpr</strong>: GROMACS binary run input (tpr) file </li> <li><strong>prod0.edr</strong>: GROMACS energy (edr) file</li> <li><strong>prod0.gro</strong>: GROMACS output coordinates and velocities after 1 microsecond of simulation</li> <li><strong>prod0.cpt</strong>: GROMACS checkpoint file after 1 microsecond of simulation</li> <li><strong>noW.pdb</strong>: The pdb file of the starting coordinates with all water molecules removed</li> <li><strong>noW.xtc</strong>: GROMACS compressed trajectory (xtc) file with all water molecules removed</li> </ul> </li> </ul> </li> </ul> </li> </ul>
An Extension Trial of Inclisiran in Participants With Cardiovascular Disease and High Cholesterol
ClinicalTrials.gov study NCT03060577. IPD Sharing: YES. Countries: 5. Publications: 2.
Management of LDL-cholesterol With Inclisiran + Usual Care Compared to Usual Care Alone in Participants With a Recent Acute Coronary Syndrome
ClinicalTrials.gov study NCT04873934. IPD Sharing: YES. Countries: 1. Publications: 0.
CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of cholesterol, T=303K
<p>Simulation of POPC and 50%POPC+50%cholesterol bilayer in full hydration (40 water/lipid) at T=303K in NPT ensemble. Simulations where done on GPU Gromacs 2020.1. The initial configurations and force field (CHARMM36) were dowloaded from CHARMM-GUI. Simulation uses Parrinello-Rahman barostat and Nose-Hoover thermostat.</p>
Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations
<p>Input files, topologies and trajectories of the work "Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations". </p>
Dimensions, stability and deformability of DOPC-cholesterol Giant Unilamellar Vesicles formed by droplet transfer – Extended Data
<p>This dataset contains the Underlying Data to the paper “ Dimensions, stability and deformability of DOPC-cholesterol Giant Unilamellar Vesicles formed by droplet transfer”.</p> <ul> <li> “deformation_size” folder containing scatter plots of σ with respect to GUVs rest radii <ul> <li>sd_deform_scatter_H1</li> <li>sd_deform_scatter_H2</li> <li>sd_deform_scatter_H3</li> </ul> </li> <li>“magnetic_device_support” folder containing the .stl files for 3D-printing the magnets-support of the magnetic device <ul> <li>magnetic_device_support_part1</li> <li>magnetic_device_support_part2</li> </ul> </li> <li>“size_distribution_magnetic” folder containing size distribution histograms comparing 100:0 DOPC:cholesterol and 60:40 DOPC:cholesterol samples, under the application of magnetic fields <ul> <li>sd_magnetic_size_dist_allfields</li> <li>sd_magnetic_size_dist_H1</li> <li>sd_magnetic_size_dist_H2</li> <li>sd_magnetic_size_dist_H3</li> </ul> </li> <li>“size_distribution_T0vsON” folder containing size distribution histograms comparing pristine samples (t<sub>0</sub>) and samples after overnight storage (ON), for different DOPC:cholesterol ratios <ul> <li>sd_size_dist_60_40</li> <li>sd_size_dist_71_29</li> <li>sd_size_dist_85_15</li> <li>sd_size_dist_100_0</li> </ul> </li> </ul>
NEOtrap data with cholesterol functionalized DNA origami spheres
<p>Source data used in the manuscript:<br> Orientation-locked DNA origami improves single-protein trapping in the NEOtrap</p> <p>The measurements were implemented in 600 KHM buffer under the bias voltage of 100 mV.<br> Names of these files specify the trapped protein's name with corresponding measurement conditions, i.e.,<br> bare origami sphere, Cholesterol functionalized sphere in vertical configuration, and Cholesterol functionalized sphere in horizontal configuration<br> </p>
Molcular Dynamics Trajectories for GPR156 PG No Cholesterol
<p>Note the cholesterol between the dimers were not modelled in these trajectories. Obsolete.</p> <p> </p> <p>This is not the Molecular Dynamics Data for 10.1038/s41594-024-01224-7 for publication at</p> <p>Shin, J., Park, J., Jeong, J. <em>et al.</em> Constitutive activation mechanism of a class C GPCR. <em>Nat Struct Mol Biol</em> (2024). https://doi.org/10.1038/s41594-024-01224-7</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.5 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>But please cite us if you still find this data useful!</p>
Glutamine sensing licenses cholesterol synthesis.
<p>The uploaded metabolomic dataset contains liquid-chromatography-mass spectrometry (LC-MS) data associated to a publication of Bruna Martins Garcia et al. from the Lena Pernas laboratory.</p> <p>The title olf the article is: <strong>Glutamine sensing licenses cholesterol synthesis.</strong></p> <p>This article is to be published 2024 in the EMBO Journal-</p> <p>Abstract of the article: The mevalonate pathway produces essential metabolites such as cholesterol. Although this pathway is negatively regulated by metabolic intermediates, little is known of the metabolites that positively regulate its activity.<em> </em>We found that the amino acid glutamine is required to activate the mevalonate pathway. Glutamine starvation inhibited cholesterol synthesis and blocked transcription of the mevalonate pathway—even in the presence of glutamine derivatives such as ammonia and a-ketoglutarate. We pinpointed this glutamine-dependent effect to a loss in the ER-to-Golgi trafficking of SCAP that licenses the activation of SREBP2, the major transcriptional regulator of cholesterol synthesis. Both enforced Golgi-to-ER retro-translocation and the expression of a nuclear SREBP2 rescued mevalonate pathway activity during glutamine starvation. In a cell model of impaired mitochondrial respiration in which glutamine uptake is enhanced, SREBP2 activation and cellular cholesterol were increased. Thus, the mevalonate pathway senses and is activated by glutamine at a previously uncharacterized step, and the modulation of glutamine synthesis may be a strategy to regulate cholesterol levels in pathophysiological conditions. </p> <p>The associated data in this repository is grouped according to the figures in the the above mentioned article. Each zip folder contains the LC-MS raw files and one or more Excel tables describing the parameters (retention time, observed molecular weight, detected error to expected molecular weight, signal-to-noise and the integrated raw values of the detected compounds. Material and Method utilized for the analysis of the diverse samples is available in the context of the above mentioned article.</p>
Utilizing Digital Information for Personalized Cholesterol Management
<p><span>Patients with diseases due to high cholesterol levels in Indonesia can be said to be high because, in 2022, sufferers of the disease reached 28%, with 7.9% of people dying. The problem in this study is the need for more understanding, awareness, and ability of the community to manage and maintain cholesterol through digital information, especially social media. This research uses a questionnaire to understand the community's needs and supporting factors in digitally managing cholesterol through social media. This research gathered data using purposive sampling through a Google Form questionnaire. The data collection was conducted in April 2024 in various cities in Indonesia and successfully collected 221 responses. The method used to analyze the data in this study is the Structural Equation Model (SEM) using Smart Partial Least Square (Smart-PLS) 4.0 as the analysis approach. In this study, there are ten variables with five indicators each, and there are 11 hypotheses. The outcomes of this study show that all of the indicators were valid and reliable, with all hypotheses having a significant effect. Indonesian people must be able to utilize digital information to increase knowledge and understanding about health, especially about Cholesterol Management, so that the number of people affected by disease and who die from cholesterol can be reduced.</span></p>
Simulations for: The Energetics and Ion Coupling of Cholesterol Transport Through Patched1
<p><strong>Free energy profiles:</strong></p> <p>Coarse-grained (CG) potential of mean force (PMF) free energy and histogram outputs, obtained via the gromacs weighted-histogram analysis method (WHAM). PMF profile numbers match those described in the accompanying manuscript for cholesterol movement between the:</p> <p>- PTCH1-molA ECD base and the sterol binding domain (SBD) (PMF_1a_PTCH1_molA-SHH_cholesterol)</p> <p>- PTCH1-molB ECD base and the SBD (PMF_1a_PTCH1_molB-free_cholesterol) </p> <p>- PTCH1-molA ECD base and the sterol sensing domain (SSD) (PMF_1b_PTCH1_molA-SHH_cholesterol)</p> <p>- PTCH1-molA SSD and the membrane (PMF_2_PTCH1_molA-SSD_cholesterol_OHup)</p> <p>- PTCH1-molB SSD and the membrane (PMF_2_PTCH1_molB-SSD_cholesterol_OHup)</p> <p>- PTCH1-molB SSD and the membrane in a flipped conformation (PMF_2_PTCH1_molB-SSD_cholesterol_OHdown)</p> <p>- Membrane and solvent (PMF_3_Membrane_cholesterol)</p> <p>- PTCH1-molA SBD and the solvent (PMF_4_PTCH1_molA-SSH_cholesterol)</p> <p>- PTCH1-molB SBD and the solvent (PMF_4_PTCH1_molB-free_cholesterol)</p> <p>2000 rounds of Bayesian Bootstrapping were performed.</p> <p><strong>File description for each system:</strong></p> <p>- histo.xvg: umbrella window histograms</p> <p>- bsres.xvg: Average free energy profile and computed bootstrapping error. </p> <p> </p> <p><strong>Atomistic simulations:</strong></p> <p>Subset of atomistic molecular dynamics simulations of wild-type (WT) Patched1 (PTCH1) and Dispatched1 (DISP1) in distinct ion-bound states:</p> <p>- PTCH1 with Na+ bound at Site 1 initially (PTCH1_WT_Na_Site1)</p> <p>- PTCH1 apo in 0.15 M NaCl (PTCH1_WT_apo_inNaCl)</p> <p>- PTCH1 apo in 0.15 M KCl (PTCH1_WT_apo_inKCl)</p> <p>- PTCH1 with 3 x Na+ ions bound to anionic triad residues (PTCH1_WT_3xNa)</p> <p>- PTCH1 with 3 x K+ ions bound to anionic triad residues (PTCH1_WT_3xK)</p> <p>- DISP1 apo in 0.15 M NaCl (DISP1_WT_apo)</p> <p>- DISP1 with 3 x Na+ ions bound to anionic triad residues (DISP1_WT_3xNa)</p> <p>- DISP1 with 2 x Na+ ions bound, generated by sequential ion removal from the end of DISP1_WT_3xNa simulations (DISP1_WT_2xNa)</p> <p>- DISP1 with 1 x Na+ ion bound, generated by sequential ion removal from the end of DISP1_WT_2xNa simulations (DISP1_WT_1xNa)</p> <p>- DISP1 without Na+ bound, generated by sequential ion removal from the end of DISP1_WT_1xNa simulations (DISP1_WT_0xNa)</p> <p>All simulations were run for 3 x 100 ns except for PTCH1_WT_apo_inNaCl which was run for 3 x 50 ns. The PTCH1 and DISP1 conformations were obtained from the Protein Data Bank (PDB IDs: 6DMY, 7RPH). </p> <p><strong>File description for each system:</strong></p> <p>- md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). </p> <p>- md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number). </p>
Trial to Evaluate the Effect of Inclisiran Treatment on Low Density Lipoprotein Cholesterol (LDL-C) in Subjects With Heterozygous Familial Hypercholesterolemia (HeFH)
ClinicalTrials.gov study NCT03397121. IPD Sharing: Not stated. Countries: 8. Publications: 2.
Study Of The Effects Of Atorvastatin On Cholesterol Levels In Rheumatoid Arthritis Patients Taking CP-690,550
ClinicalTrials.gov study NCT01059864. IPD Sharing: Not stated. Countries: 2. Publications: 12.
Efficacy and Safety of Colesevelam in Pediatric Patients With Genetic High Cholesterol
ClinicalTrials.gov study NCT00145574. IPD Sharing: Not stated. Countries: 8. Publications: 1.
Effect of a Treatment With a Nutraceutical Combination on Sub-optimal LDL Cholesterol Levels
ClinicalTrials.gov study NCT03739242. IPD Sharing: NO. Countries: 1. Publications: 1.
Evaluation of LDL Cholesterol in Patients Switched From 10 to 5 Milligrams of Zetia (Ezetimibe)
ClinicalTrials.gov study NCT00762229. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
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.