Raw Lipidomics Dataset for: "Perturbation of de novo lipogenesis hinders MERS-CoV assembly and release, but not the biogenesis of viral replication organelles"
Description
The dataset contains the raw values as obtained from a targeted lipidomics analysis, which was part of the study "Perturbation of de novo lipogenesis hinders MERS-CoV assembly and release, but not the biogenesis of viral replication organelles". The experimental aim was the analysis of lipidome changes on lipid class level. The values represent the relative abundance of each lipid class compared to the total lipidome. For this study, Huh7 cells were treated with a small molecule inhibitor (TOFA) and lipidome changes were compared to the levels of DMSO-treated control cells. The file contains the raw values of the TOFA-treated Huh7 cells, DMSO-treated cells, untreated Huh7 cells and standards used (blanks, quality control cells and quality control plasma). Our findings suggested a metabolic switch towards lipolysis due to the compound's mechanism of action. For further information over the data acquisition method please refer to the materials and methods and the Targeted Lipidomics Analysis section of the study, as posted on bioRxiv (DOI: https://doi.org/10.1101/2024.08.21.608937). A revised version of the study is currently submitted/under revision.
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Steps to reproduce
For steps to reproduce the data acquisition method, please check the materials and methods and the Targeted Lipidomics Analysis section of the manuscript, as posted on bioRxiv (DOI: https://doi.org/10.1101/2024.08.21.608937). Description of the experimental set up and a copy of the materials and methods section can be found below: Huh7 cells were treated with DMSO or 10 μM TOFA. The amounts of intracellular lipids were determined by mass spectrometry 12 h after compound addition. Comprehensive, quantitative shotgun lipidomics was carried out as described in detail elsewhere (77, 78). Briefly, samples were spiked with deuterated internal standards and lipids were extracted using methyl tert-butyl ether. The combined organic extracts were subsequently dried under a gentle stream of nitrogen and the dried extracts were dissolved in methanol:chloroform 1:1 containing 10 mM ammonium acetate. Lipids were then analyzed with a flow injection method at a flow rate of 8 µL/min applying differential ion mobility for lipid class separation and subsequent multiple reaction monitoring in positive and negative electrospray ionization mode. Using the Shotgun Lipidomics Assistant (SLA) software individual lipid concentrations were calculated after correction for sample input and their respective internal standards. (77) Su B, Bettcher LF, Hsieh W-Y, Hornburg D, Pearson MJ, Blomberg N, Giera M, Snyder MP, Raftery D, Bensinger SJ, Williams KJ. 2021. A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics. Journal of the American Society for Mass Spectrometry 32:2655-2663. (78) Ghorasaini M, Mohammed Y, Adamski J, Bettcher L, Bowden JA, Cabruja M, Contrepois K, Ellenberger M, Gajera B, Haid M, Hornburg D, Hunter C, Jones CM, Klein T, Mayboroda O, Mirzaian M, Moaddel R, Ferrucci L, Lovett J, Nazir K, Pearson M, Ubhi BK, Raftery D, Riols F, Sayers R, Sijbrands EJG, Snyder MP, Su B, Velagapudi V, Williams KJ, de Rijke YB, Giera M. 2021. Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring. Analytical Chemistry 93:16369-16378 For figure preparation, the data values were plotted using Graphpad prism v.10 and represented as mean ± SD of the three biological replicates. Statistical significance was calculated using unpaired Student’s t-test, where * p<0.05, ** p< 0.01, *** p< 0.001, **** p< 0.0001.