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75 results for “Plasma proteins”
Amine metabolites in pigs fed a diet with spray dried plasma protein as functional protein source
<p><span>We evaluated the effects of diets formulated with either soybean meal (SBM) as a reference protein source or SDPP in pigs. Blood amine profiles were analysed to evaluate the effects of the diets at a systemic level. <span>Blood samples were collected via the ear-vein for plasma preparation at at dissection days (d28-29) after the morning meal ingestion. </span></span></p> <p><span>For plasma, blood samples were collected in sterile Vacuette tubes containing lithium-heparin and immediately centrifuged at 3,000x g for 10 min at 4°C and plasma was extracted. Plasma were stored at -80°C for further analysis on levels ofsystemic amine metabolite profiles. </span></p> <p>The protocol outlined in the following publication was used for detecting plasma amine levels:</p> <ul> <li>Noga MJ, Dane A, Shi S, Attali A, van Aken H, Suidgeest E, et al. Metabolomics of cerebrospinal fluid reveals changes in the central nervous system metabolism in a rat model of multiple sclerosis. <span><span><span>Metabolomics. 2012;8(2):253-63.</span></span></span></li> <li><span><span><span>van der Kloet FM, Bobeldijk I, Verheij ER, Jellema RH. </span></span></span>Analytical Error Reduction Using Single Point Calibration for Accurate and Precise Metabolomic Phenotyping. Journal of Proteome Research. 2009;8(11):5132-41.</li> </ul>
A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane
<p>This upload contains files documented in a preprint and a publication.</p> <p>Preprint: https://doi.org/10.1101/2022.03.30.486314</p> <p>Publication: <a href="https://doi.org/10.1073/pnas.2205425119">https://doi.org/10.1073/pnas.2205425119</a></p> <p>The files uploaded here are:</p> <p>- Alphafold predictions for VPS13A N-term (a.a. 1-2100) and C-term (a.a. 1021-3174). The .pse file is the pymol structure alignment of the two predicted VPS13A portions, join at aminoacid position D14 with the different representations presented throughout the paper stored as pymol "scenes". </p> <p>- AlphaFold-Multimer prediction for the interaction between XK and the C-term region of VPS13A is also included.</p> <p>- An excel file containing the tabular data for the graphs in Figures 1G, S2E and 4D.</p>
The state-of-the-art machine learning model for Plasma Protein Binding Prediction: computational modeling with OCHEM and experimental validation
<p><span>Institute of Materia Medica, Chinese Academy of Medical Sciences purchased 10,000 ChemDiv databases.</span></p>
Summary statistics of cis-pQTLs for plasma proteins measured using Olink Explore I and II technology in the KARMA cohort.
<p>This data set contains summary statistics for cis regions (+/- 1 Mb around the protein coding gene) for proteins measured by the Olink Explore I and II technology in pre-diagnostic plasma samples from 299 Breast Cancer cases and 299 Breast Cancer free controls from the KARMA cohort. Only proteins detected in at least 25% of individuals are included in this data set. Data set from <a href="https://www.researchsquare.com/article/rs-2749047/v1">Evaluation of Circulating Plasma Proteins in Breast Cancer: A Mendelian Randomization Analysis | Research Square</a></p>
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
<p>Here we present NMR and MS data used in article A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein. NMR data contain full set of assignment experiments used to partially assign signals of non-myristoylated wt M-PMV MAPPHis, H-N HSQC spectra or myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and results from TALOS+ program used to calculate the secondary structure of C-terminal part of both mristoylated and non-myristoylated wt MAPPHis. The MS data contain MS data measured both for non-labeled samples of myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and non-myristoylated MAPPHis, as well as data measured on these proteins after deuterium exchange.</p>
Using protein isolation on elasmobranch blood plasma for ecological research and stable isotope analysis
<p>Stable isotope analysis is a useful tool for studying the ecology of elasmobranchs. Analysis of elasmobranch blood plasma provides insight into an individual's ecology on a small temporal scale. However, plasma is a systemic transport vessel containing many dissolved constituents in variable amounts, which may bias analyses and ecological conclusions based on that data.</p> <p>In this study, we develop a new method of protein precipitation using ethanol and acetonitrile to isolate the protein fraction of plasma from Sandbar Sharks, and examine its effects on carbon and nitrogen stable isotope values. We also tested these solvent precipitations on bovine serum albumin as a control to assess the introduction of exogenous sources of C and N.</p> <p>Protein isolation resulted in a significant decrease in δ<sup>13</sup>C values and a significant increase in C:N compared to untreated plasma. Isolated proteins were not significantly different in δ<sup>15</sup>N value compared to untreated plasma. We observed no change in isotope composition in bovine serum albumin samples, indicating protein precipitation does not itself affect isotope analysis.</p> <p>These results suggest that the preparation of blood plasma is necessary for stable isotope analysis, to eliminate the biasing effects of other dissolved compounds. We find that solvent precipitation is an effective method of isolating proteins for stable isotope studies.</p>
Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation - ESI
<p>ESI data for the paper 'Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation'.</p>
Concentration of selected proteins in plasma of patient with soft tissue infections or sepsis
<p>The dataset includes two tabular sets of concentration measurements of selected proteins in plasma samples from patients with soft tissue infections or sepsis. Patients with soft tissue infections are classified into three groups: Patients with necrotizing soft tissue infections (NSTI), suspected NSTI cases but where no necrotic tissue was found during surgical exploration (Non-NSTI) and cellulitis. The sepsis patient cohort has heterogeneous etiologies and location of infection. Additionally, we included a group of patients that had surgery related to non-infectious conditions as a healthy cohort of patients (Surgical control).</p> <p>The measurements were performed by Luminex® multiplex immunoassay or ELISA. Each of the two sets were obtained from independent rounds of measurements and differ in the panel of analytes measured and samples included. The first set of measurements (Set01) covers 39 analytes measured in two sets of customized multiplex plates (32-plex and 5-plex), and two in independent ELISA assays. These analytes were measured in 251 NSTI samples, 20 Non-NSTI, 19 cellulitis and 20 surgical controls. The second set of measurements (Set02) consist of a subset of 10 analytes included in the first set and were measured in two multiplex plates (4-plex and 6-plex). The second round of measurements were carried out in 60 additional NSTI patients and 24 sepsis patients.</p> <p>Lastly, imputation of censored data was carried out only in the first set of measurements and the resulting data is also available in the current data set (Set01_imputed).</p>
Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
<p>Full results datasets for Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility:</p> <p>ALL*all_pheno.csv are TOPMed-MESA combined-ancestry models, discovery and replication cohorts</p> <p>ARIC_EA_all_pheno.csv is ARIC European-American ancestry models, discovery cohort</p> <p>ARIC*meta_all.txt is ARIC European-American ancestry models, discovery and replication cohorts, with meta-analysis of disc+rep</p>
LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-A"
<p>LC-MS/MS data generated from plasma samples from children with bacterial and viral infections. </p>
LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-B"
<p>LC-MS/MS data generated from plasma samples from children with bacterial and viral infections. </p>
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from <em>Arabidopsis thaliana </em>is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.</p>
Trial of Mesna to Prevent Doxorubicin-induced Plasma Protein Oxidation and Tumor Necrosis Factor Alpha (TNF-α) Release
ClinicalTrials.gov study NCT01205503. IPD Sharing: YES. Countries: 1. Publications: 1.
Effect of Human Plasma Protein Transfusion With and Without Crystalloids During Major Liver Resection Surgeries
ClinicalTrials.gov study NCT05033704. IPD Sharing: YES. Countries: 1. Publications: 12.
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
Open the record for dataset details and reuse information.
Methods for precipitating plasma proteins for stable isotope analysis of elasmobranch blood
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Concentration of selected proteins in plasma of patient with soft tissue infections or sepsis
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i-Tasser 3D Strucutres of Blood Plasma Proteins for United Atom Multiscale Modelling Of Bio-Nano Interactions
<p>3D Structures of blood plasma proteins as per proteomic data on protein corona for AgNPs presented in this publication:</p> <blockquote> <p>Gorshkov V, Bubis JA, Solovyeva EM, Gorshkov M, KjeldsenF. Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution. Environ. Sci.: Nano, 2019,6, 1089-1098. doi: 10.1039/C8EN01054D</p> </blockquote> <p>Note, that the dataset is different from the one used in this publication:</p> <blockquote> <p>Alsharif SA, Power D, Rouse I, Lobaskin V. In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles. Nanomaterials (Basel). 2020 Oct 4;10(10):1967. doi: 10.3390/nano10101967.</p> </blockquote> <p>Files were prepared with I-TASSER utility:</p> <blockquote> <p>J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015).</p> </blockquote> <p> </p>
Impact of Canola Protein Processing on Plasma Amino Acid Responses
ClinicalTrials.gov study NCT06058403. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect of Osteopathic Lymphatic Treatment on Plasma Volume, Protein Concentration and Albumin Concentration.
ClinicalTrials.gov study NCT00742989. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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International Brain Laboratory public data
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OpenNeuro
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