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104 results for “Ceramides”
Lab_26_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_26_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_13_OTHER_neg - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_13_OTHER_neg - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_25_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_25_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_21_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_21_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction - buil and Analysis
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> All scripts, jupyter notebooks, and data files used to building and analyzing systems in the presented in the paper. Also related experimental data.</p>
Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"
<p>Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. <em>PLoS Comput. Biol.</em> <strong>2023</strong>, <em>19</em>, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.</p>
iTRAQ proteomics dataset on ceramide-dependent exosomal cargoes from SW480 and SW620 cells
Open the record for dataset details and reuse information.
Structural basis of the mechanism and inhibition of a human ceramide synthase
<p><em>This dataset comprises the raw LC-MS and LC-MS/MS data files that underpin the mass spectral analysis detailed in our publication, “Structural Basis of the Mechanism and Inhibition of a Human Ceramide Synthase.” For ease of navigation and to match each raw data file with its corresponding spectrum in the paper, please refer to the provided Excel spreadsheet Updated_V2<br></em></p>
Lab_02_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_02_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1> <p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank" rel="noopener">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p> <p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="../doi/10.5281/zenodo.10081970" target="_blank" rel="noopener">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank" rel="noopener">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="../doi/10.5281/zenodo.10081970" target="_blank" rel="noopener">here</a>.</p> <p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_32_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_32_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Fig. 6 in Undescribed glucosylceramide, flavonol triglycoside, and oleanane saponin from the halophyte Agathophora alopecuroides: Promising candidates for stimulating ceramide synthesis
Fig. 6. Effect of isolated compounds (1–11) and methanol extract of A. alopecuroides (12) on mRNA expression levels of CerS3 involved in ceramide synthesis in HaCaT cells. HaCaT cells were cultured in the presence or absence of tested samples at 10–400 μg/mL for 24 h. RT-PCR analysis was performed as described in Material and methods part. Data are expressed as means ± SD of at least three independent experiments; *p <0.05, **p <0.01.
Fig. 5 in Undescribed glucosylceramide, flavonol triglycoside, and oleanane saponin from the halophyte Agathophora alopecuroides: Promising candidates for stimulating ceramide synthesis
Fig. 5. Effect of extract and isolated compounds on viability of HaCaT cells. A: Compounds 1–3; B: Compounds 4–6; C: Compounds 7–9; D: Compounds 10–11 and methanol extract (12). Cell viability was measured by MTT assay. HaCaT cells (1 105 cells/well) were seeded to a 96-well plate and incubated overnight. The cell × viability was performed after treatment with extract and isolated compounds (1–400 μg/mL) for 24 h. Values are expressed as the mean ± SD of three wells; *p <0.05, **p <0.01.
Fig. 4 in Function of ceramide synthases on growth, ganoderic acid biosynthesis and sphingolipid homeostasis in Ganoderma lucidum
Fig. 4. Ganoderic acid biosynthesis in G. lucidum is influenced by the lag gene. A Systematic content analysis of ganoderic acid in the lag-silenced, WT and SiControl strains. B–D Relative gene expression of hmgr (B), sqs (C) and osc (D) in the WT, SiControl and lag-silenced strains. There are three independent biological replicates in each column. Error bars represent standard deviations, and asterisks show significant differences from control (WT and Sicontrol) strains according to Student's t-test (**P <0.01, n = 3).
Fig. 3 in Function of ceramide synthases on growth, ganoderic acid biosynthesis and sphingolipid homeostasis in Ganoderma lucidum
Fig. 3. Effect of lag gene silencing on G. lucidum growth. Morphology of fungal colonies in lag-silenced, WT and SiControl strains after cultivation in the dark on CYM medium at 28 ̊C for 5 days. Three independent biological replicates in each column. Error bars represent standard deviations, and asterisks show significant differences from control (WT and Sicontrol) strains according to Student's t-test (**P <0.01, n = 3).
Fig. 1 in Function of ceramide synthases on growth, ganoderic acid biosynthesis and sphingolipid homeostasis in Ganoderma lucidum
Fig. 1. Overview of the sphingolipid biosynthetic pathway in yeast and filamentous fungi. The abbreviations used are as follows: Dihydroxy LCB: dihydroxy longchain (sphingoid) base; Trihydroxy LCB: trihydroxy long-chain sphingoid base; Long chain FA-CoA: long chain fatty acyl-coenzyme A; Very long chain FA-CoA: very long chain fatty acyl-coenzyme A; IPC synthase: inositol phosphorylceramide synthase; IPC mannosyl transferase: inositol phosphorylceramide mannosyl transferase; MIPCs: mannose inositol phosphorylceramides; M (IP)2Cs: mannose (inositol phosphoryl)2- ceramides.
Fig. 2. G in Function of ceramide synthases on growth, ganoderic acid biosynthesis and sphingolipid homeostasis in Ganoderma lucidum
Fig. 2. G. lucidum harbours three ceramide synthases. Phylogenetic analysis of ceramide synthases in eukaryotes. The phylogenetic tree was conducted using MEGA 6 and can be roughly divided into three major groups: human, plant and fungi. The evolutionary history was inferred by the neighbour-joining method from 1000 replicates using MEGA 6.
Fig. 5 in Function of ceramide synthases on growth, ganoderic acid biosynthesis and sphingolipid homeostasis in Ganoderma lucidum
Fig. 5. Sphingolipid profiling of the lag-silenced, WT and SiControl strains. The relative amounts of Cer (A), GlcCer (B), IPC (C), MIPC (D) and M (IP)2C (E) in each strain. Comparison of the sphingolipid intensity ratios between the WT and lag-silenced strains. Each sphingolipid (Cer/GlcCer/IPC/ MIPC/M(IP)2C) intensity ratio was calculated as the percentage of the corresponding total sphingolipid detected in the WT or mutant. The sphingolipid species are indicated as the number of carbon atoms: the unsaturated bond number of the fatty acid: hydroxyl number. For example, Cer 32:0:2 = Cer (d18:0/14:0); Cer 36:0:3 = Cer (t18:0/18:0 or d18:0/18:0 (2-OH)); Cer 36:0:4 = Cer(t18:0/18:0 (2-OH)); Cer 38:1:2 = Cer (d18:0/20:1 or d18:1/ 20:0) and Cer 42:2:2 = (d18:0/24:2, d18:2/24:0 or d18:1/24:1). There are three independent biological replicates in each column. Error bars represent standard deviations, and asterisks show significant differences from control (WT and Sicontrol) strains according to Student's t-test (*P <0.05, **P <0.01, n = 3).
Ceramide Level as Apredictor of Outcomes in Patients of Anterior Myocardial Infarction Undergoing Primary Coronary Intervention
ClinicalTrials.gov study NCT04572191. IPD Sharing: Not stated. Countries: 1. Publications: 4.
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