Workflow4Metabolomics Object Identifier: W4M00006
Digital Object Identifier: 10.15454/1.4821558812795176E12
Creator of the history: Marie Tremblay-Franco
Maintainer: Marie Tremblay-Franco (marie.tremblay-franco at inra.fr)
Creation|Updating date: 2016-11-25
Format: Workflow4Metabolomics Galaxy histories
W4M History: https://workflow4metabolomics.usegalaxy.fr/histories/list_published
Size: 7 Mo
Keywords: musmusculus, brain, BPA, NMR, preprocessing, statistics, annotation
Description:
| Study: Metabolic shifts induced in vivo after perinatal exposure to low doses of BPA in CD-1 mice were assessed. In this study conducted by the ToxAlim-MeX team and the Tufts University school of medicine (Boston, MA, USA) in collaboration with the AXIOM-MetaToul-MetaboHUB platform, aqueous brain extracts from twenty-four 21-day-old pups whose mothers were exposed to either 0.025µg or 0.25µg BPA/kg BW/day during gestation and lactation were analyzed by NMR Spectroscopy. |  |
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Dataset: The dataset contains 24 Bruker files preprocessed using the TopSpin software (Bruker): Fourier Transformation was applied to free induction decays, then all the NMR spectra were phased and the baselines were corrected and calibrated with the TopSpin software. |
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Workflow: The workflow consists in the following steps: fixed-size bucketing (0.01ppm), normalization by the total intensity of the spectrum, Pareto scaling, PCA to detect outliers, OPLS-DA modeling of BPA dose, univariate hypothesis testing of significant variations with BPA dose (FDR < 0.05) for discriminant buckets (OPLS-DA VIP > 0.8), and metabolite annotation with the NMR Annotation tool. On the figure: from animal experimentation to metabolites annotation: upper left: experimental design and brain sampling; upper middle: sample preparation (brain extraction); upper right: NMR spectra acquisition (Bruker files); middle right: data reduction (bucketing + normalization); lower: multivariate analysis (PCA and O-PLS-DA score plots, permutation test); middle left: correspondence between univariate testing (bucket with VIP value > 0.8) and metabolite annotation. |
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Comments: Please note that this pairwise comparison was not presented in the publication by Cabaton et al. (2013). |
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Rights: Creative Commons
Citations:
- Cabaton NJ, Canlet C, Wadia PR, Tremblay-Franco M, Gautier R, Molina J, Sonnenschein C, Cravedi JP, Rubin BS, Soto A, Zalko D. Effects of low doses of Bisphenol A on the metabolome of perinatally exposed CD-1 mice. Environmental Health Perspectives 2013;121: 586-593. DOI:10.1289/ehp.1205588.
Raw data repository:
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