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.
1,108
datasets available to search
ShareScore release 0.9.0
Dataset results
1,108 results for “Metabolomics”
NMR spectroscopy-based metabolomics of organotypic retinal explants
<p>The retina consumes massive amounts of energy, yet its metabolism and substrate exploitation remain poorly understood. Here, we used a murine explant model to manipulate retinal energy metabolism under entirely controlled conditions and utilized <sup>1</sup>H-NMR spectroscopy-based metabolomics, in situenzyme detection, and cell viability readouts to uncover the pathways of retinal energy production. Our experimental manipulations resulted in varying degrees of photoreceptor degeneration, while the inner retina and retinal pigment epithelium were essentially unaffected. This selective vulnerability of photoreceptors suggested very specific adaptations in their energy metabolism. Rod photoreceptors were found to rely strongly on oxidative phosphorylation, but only mildly on glycolysis. Conversely, cone photoreceptors were dependent on glycolysis but insensitive to electron transport chain decoupling. Importantly, photoreceptors appeared to uncouple glycolytic and Krebs-cycle metabolism via three different pathways: 1) the mini-Krebs-cycle, fueled by glutamine and branched-chain amino acids, generating N-acetylaspartate; 2) the alanine-generating Cahill-cycle; 3) the lactate-releasing Cori-cycle. Moreover, the metabolomic data indicated a shuttling of taurine and hypotaurine between the retinal pigment epithelium and photoreceptors, likely resulting in an additional net transfer of reducing power to photoreceptors. These findings expand our understanding of retinal physiology and pathology and shed new light on neuronal energy homeostasis and the pathogenesis of neurodegenerative diseases.</p>
Metabolome data of fresh and conditioned in vitro oocyte maturation media and blastocyst conditioned media
<p>This dataset includes metabolome profiles from fresh and conditioned in vitro maturation media and blastocyst conditioned media. Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry was performed on media samples and Xcalibur (RAW) files were converted to an open source mzML format (msconvert software; ProteoWizard package). The converted files were processed using the Metabolomic Analysis and Visualization Engine (MAVEN; mzroll software, Princeton University) to complete an untargeted analysis of the liquid chromatography mass spectrometry data. The pre-processed peak data tables generated by MAVEN are provided in this dataset.</p>
Tandem Mass Spectrometry Dataset for Machine Learning in Metabolomics
<p>This dataset contains tandem mass spectrometry data cleaned and processed from the publicly available GNPS Spectral Library. We aim to continuously update this dataset with new data points as the spectral libraries expand.</p>
The metabolomics raw data and a supporting statistical analyses data set for publication: Metabolomic analysis revealed the absence of the principal antimicrobial compound of Pseudomonas donghuensis P482, 7-hydroxytropolone, under restricted nutrient conditions.
<p><a href="../api/records/11220997/draft/files/Metabolomic%20analyses%20raw%20files.zip/content" target="_blank" rel="noopener noreferrer">Metabolomic analyses raw files</a>, Compounds analyses, Hierarchical Condition tress and PCA Scores are uploaded.</p>
Metabolomic analysis of cultured TRAMP-C2 cells in the presence or absence of PD-L1 expression
<p>The interaction between the immune inhibitory receptor PD-1 and its ligand PD-L1 is a critical mechanism for altering immune responses, especially during chronic antigen exposures such as cancer. While much research has focused on the PD-1 receptor, recent evidence suggests that PD-L1 can have cell-intrinsic effects in cancer and immune cells. These functions are distinct from its ability to bind and trigger PD-1 activity and are notable given that PD-L1 is widely expressed in mammals. One such cell-intrinsic function is the modulation of cellular metabolism, including regulation of mTOR activity and glycolysis. As part of our investigation into PD-L1 function, we analyzed the metabolome of cultured mouse prostate cancer cells (TRAMP-C2) expressing PD-L1 or with PD-L1 deleted via CRISPR/Cas9. We quantified 186 water-soluble metabolites from TRAMP-C2 cells expressing PD-L1 or not to better understand what metabolic pathways and processes are regulated by PD-L1 expression/activity. We found a broad range of differentially abundant metabolites, most notably a decreased abundance of glycolytic metabolites when PD-L1 expression is knocked out. In our manuscript, we show that this has a functional outcome on viral infection and cytokine signaling.</p>
Figure 2 in Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches
Figure 2. Workflow of transcript analyses by RNA-Seq and qRT-PCR.
An advanced metabolomic approach untangles oviposition preference of grape skin by Drosophila suzukii
Open the record for dataset details and reuse information.
Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Metabolomics Data
<p>Polar metabolomics data (targeted and untargeted) used for analysis of microbial community function over a diurnal cycle in Lemonade Creek, Yellowstone National Park, USA.</p> <p> </p> <p><code>GNPS_positive-2.xlsx</code> Comparison of GNPS data used for main metabolite analysis with targeted metabolite features. Done to support the accuracy of the GNPS results for metabolites identified outside the targeted set.</p> <p> </p> <p><code>NEG_506963_FinalEMA-HILIC_Identifications.xlsx</code> Negative ionization targeted metabolite identification quality and confidence results (prepared by the Joint Genome Institute, USA).</p> <p><code>NEG_msms_mirror_plots.tar.gz</code> Negative ionization targeted metabolite mirror plots.</p> <p><code>NEG_peak_height.tab</code> Negative ionization targeted metabolite peak height file (main results file used for abundance analysis).</p> <p><code>POS_506963_FinalEMA-HILIC_Identifications.xlsx</code> Positive ionization targeted metabolite identification quality and confidence results (prepared by the Joint Genome Institute, USA).</p> <p><code>POS_msms_mirror_plots.tar.gz</code> Positive ionization targeted metabolite mirror plots.</p> <p><code>POS_peak_height.tab</code> Positive ionization targeted metabolite peak height file (main results file used for abundance analysis).</p> <p> </p> <p><code>NEG_peak_height.csv</code> Negative ionization untargeted metabolite peak height file (main results file used for abundance analysis).</p> <p><code>POS_peak_height.csv</code> Positive ionization untargeted metabolite peak height file (main results file used for abundance analysis).</p>
Integrated Probabilistic Annotation (IPA): A Bayesian-based annotation method for metabolomic profiles integrating biochemical connections, isotope patterns and adduct relationships - Supplementary Data
<ol> <li>Supplementary_data_1: data and code for standards analysis and database update</li> <li>Supplementary_data_2.zip: data and code used for the generation of the synthetic experiment</li> <li>Supplementary_data_3.zip: data, code, and results of the <em>E. coli</em> dataset analysis</li> <li>Supplementary_data_4.zip: data, code, and results of the beer dataset analysis</li> <li>Supplementary_data_5.zip: data, code, and results of the comparison with xMSannotator</li> </ol>
Computational Metabolomics - database files for raw data processing
<p>These files are used by an R-script that process LCMS data files in a project directory to detect peaks, make the aligned peak table and annotate peaks with molecular formulas. The workflow is optimized for human blood samples (n > 100). </p>
Comparison of the phytochemical composition and bioactivity of the latex of Hura crepitans L. from Peru and Africa by metabolomic approaches
<p><em><span>Hura crepitans</span></em><span> <span> </span>(Euphorbiaceae), is widespread in the Amazon rainforest and on plantations in sub-Saharan Africa. This tree produces an irritating milky latex rich in secondary metabolites, notably daphnane-type diterpenes and cerebrosides. Previous studies have shown that huratoxin, the main daphnane in the latex, significantly and selectively inhibited the growth of colorectal cancer cells through a unique mechanism involving the activation of PKCζ. One major challenge in isolating active molecules from natural products is the accessibility of the resource. This study explores the phytochemical composition and cytotoxic activities of latexes collected in Peru, Benin, and Togo using UHPLC-MS and metabolomics tools to identify a renewable source of bioactive compounds. Significant inter- and intra-continental differences in chemical composition have been highlighted, with daphnanes being concentrated in the Peruvian samples. Extracts form latexes collected in Peru showed cytostatic activity on Caco-2 cells, correlated with the presence of daphnanes, while some African samples exhibited cytotoxic activity on Jurkat and Hela cancer cell lines, leading to the identification of potential other new bioactive compounds such as sterol and cerebrosides.</span></p> <p><span> </span></p>
Metabolomics Peak Tables of push-pull and control field maize tissue extracts
<p>Data tables of the WP3 maize extracts of the UPSCALE project. Fragment spectra are provided as mgf files.</p>
Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking
<p>Comparative analysis of SIRIUS to evaluate our method, Biotransformation-based Annotation Method (BAM). This dataset includes all scripts, data, and results relevant to this analysis. BAM can be found on GitHub (https://github.com/HassounLab/BAM). </p> <p> </p> <p> </p>
High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds
<h3><em><strong>Content</strong></em></h3> <p>Dataset of the study: "High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds.</p>
Description of metabolic differences between castrated males and intact gilts obtained from high-throughput metabolomics of porcine plasma
<h3>Content</h3> <div> <p>Dataset of the study: Description of metabolic differences between castrated males and intact gilts obtained from high-throughput metabolomics of porcine plasma.</p> <p> </p> </div>
Data from: Anopheles gambiae: metabolomic profiles in sugar-fed, blood-fed and Plasmodium falciparum-infected midgut
The mosquito midgut is a physiological organ essential for the nutrient acquisition as well as an interface that encounters various mosquito borne pathogens. Metabolomic characterization would reveal biochemical fingerprints that are generated by various cellular processes. The metabolite profiles of the mosquito midgut will provide an overview of the biochemical events in both physiological states and the dynamic responses to pathogen infections. In this study, the midgut metabolic profiles of Anopheles gambiae mosquitoes following feeding with sugar, human blood, mouse blood, and Plasmodium falciparum-infected human blood were examined. A mass spectrometry system coupled to liquid and gas chromatography produced a time series of metabolites in the midgut at discrete conditions (sugar feeding, 24hr and 48hr post normal blood and P. falciparum-infected blood feeding). Triplicates were included to ensure system validity. A total of 512 individual compounds were identified, 511 were assigned to 8 super-pathways and 75 sub-pathways. The dataset can be used for further inquiry into the metabolic dynamics of sugar and blood digestion and of malaria parasite infection.
Data from: Protection of pepper plants from drought by microbacterium sp. 3J1 by modulation of the plant's glutamine and α-ketoglutarate content: a comparative metabolomics approach
<p><span>Desiccation-tolerant plants are able to survive for extended periods of time in the absence of water. The molecular understanding of the mechanisms used by these plants to resist droughts can be of great value for improving drought tolerance in crops. This understanding is especially relevant in an environment that tends to increase the number and intensity of droughts. The combination of certain microorganisms with drought-sensitive plants can improve their tolerance to water scarcity. One of these bacteria is <i>Microbacterium </i>sp. 3J1, an actinobacteria able to protect pepper plants from drought. In this study, we supplemented drought-tolerant and drought-sensitive plant rhizospheres with <i>Microbacterium</i> sp. 3J1 and analyzed their proteomes under drought to investigate the plant-microbe interaction. We also compare this root proteome with the proteome found in desiccation-tolerant plants. In addition, we studied the proteome of <i>Microbacterium</i> sp. 3J1 subjected to drought to analyze its contribution to the plant-microbe interaction. We describe those mechanisms shared by desiccation-tolerant plants and sensitive plants protected by microorganisms focusing on protection against oxidative stress, and production of compatible solutes, plant hormones, and other more specific proteins.</span></p>
Bucket Table Edwards et al 2021 Metabolomic Markers of Storage Temperature and Time in Pasteurized Milk
<p>NMR spectroscopic data of a set of milk samples at different temperatures and storage times. Spectra were binned using AMIX 3.9.15 (Bruker BioSpin, Rheinstetten, Germany).</p>
Digesta and Plasma Metabolomics of Rainbow Trout Strains with Varied Tolerance of Plant-Based Diets Highlights Potential for Non-Lethal Assessments of Enteritis Development
<p>The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (<em>Oncorhynchus mykiss</em>) is one such species in which the strain ARS-<em>Sel</em>has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth, and plasma and digesta metabolomes between the ARS-<em>Sel</em>and two commercial strains (CS-1 and CS-2), when fed a plant-protein diet (PM) and a fishmeal-based diet (FM) and correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-<em>Sel</em>fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma metabolite profiles of ARS-<em>Sel</em>and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of the enteritis development, which was confirmed by a histological approach. In digesta, no differences were observed between groups. As reported in previous studies the ARS-<em>Sel</em>strain performed better than the commercial strains when fed the PM diet. </p>
mass spectrometry metabolomic analysis of Drosophila head extracts: 3 genotypes (control, RNAi Opa1 in muscle, RNAi Marf in muscle), 2 ages (30 days, 65 days)
<p>RNAi of the Drosophila mitochondrial fusion genes Opa1 and Marf (Mitofusin 2) in the muscle results in an extended lifespan. In order to detect metabolic changes in lipid in the neural tissue, we analysed the metabolome of fly heads by mass spectroscopy, comparing the two knock-down genotypes to a wild type control at two ages: 30 days (young flies) and 65 days (old flies).</p>
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.