A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium

Dinesh K. Barupal; Ying Zhang; Tong Shen; Sili Fan; Bryan S. Roberts; Patrick Fitzgerald; Benjamin Wancewicz; Luis Valdiviez; Gert Wohlgemuth; Gregory Byram; Ying Yng Choy; Bennett Haffner; Megan R. Showalter; Arpana Vaniya; Clayton S. Bloszies; Jacob S. Folz; Tobias Kind; Ann M. Flenniken; Colin McKerlie; Lauryl M.J. Nutter; Kent C. Lloyd; Oliver Fiehn

doi:10.3390/metabo9050101

A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium

Dinesh K. Barupal, Ying Zhang, Tong Shen, Sili Fan, Bryan S. Roberts, Patrick Fitzgerald, Benjamin Wancewicz, Luis Valdiviez, Gert Wohlgemuth, Gregory Byram, Ying Yng Choy, Bennett Haffner, Megan R. Showalter, Arpana Vaniya, Clayton S. Bloszies, Jacob S. Folz, Tobias Kind, Ann M. Flenniken, Colin McKerlie, Lauryl M.J. NutterKent C. Lloyd, Oliver Fiehn

Surgery

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Mouse knockouts facilitate the study ofgene functions. Often, multiple abnormal phenotypes are induced when a gene is inactivated. The International Mouse Phenotyping Consortium (IMPC) has generated thousands of mouse knockouts and catalogued their phenotype data. We have acquired metabolomics data from 220 plasma samples from 30 unique mouse gene knockouts and corresponding wildtype mice from the IMPC. To acquire comprehensive metabolomics data, we have used liquid chromatography (LC) combined with mass spectrometry (MS) for detecting polar and lipophilic compounds in an untargeted approach. We have also used targeted methods to measure bile acids, steroids and oxylipins. In addition, we have used gas chromatography GC-TOFMS for measuring primary metabolites. The metabolomics dataset reports 832 unique structurally identified metabolites from 124 chemical classes as determined by ChemRICH software. The GCMS and LCMS raw data files, intermediate and finalized data matrices, R-Scripts, annotation databases, and extracted ion chromatograms are provided in this data descriptor. The dataset can be used for subsequent studies to link genetic variants with molecular mechanisms and phenotypes.

Original language	English (US)
Article number	101
Journal	Metabolites
Volume	9
Issue number	5
DOIs	https://doi.org/10.3390/metabo9050101
State	Published - May 1 2019

Keywords

Functional genomics
GC-MS
IMPC
LC-MS
Lipidomics
Metabolic phenotyping
Metabolomics
Mouse knockouts

ASJC Scopus subject areas

Endocrinology, Diabetes and Metabolism
Biochemistry
Molecular Biology

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10.3390/metabo9050101

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Barupal, D. K., Zhang, Y., Shen, T., Fan, S., Roberts, B. S., Fitzgerald, P., Wancewicz, B., Valdiviez, L., Wohlgemuth, G., Byram, G., Choy, Y. Y., Haffner, B., Showalter, M. R., Vaniya, A., Bloszies, C. S., Folz, J. S., Kind, T., Flenniken, A. M., McKerlie, C., ... Fiehn, O. (2019). A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium. Metabolites, 9(5), [101]. https://doi.org/10.3390/metabo9050101

A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium. / Barupal, Dinesh K.; Zhang, Ying; Shen, Tong; Fan, Sili; Roberts, Bryan S.; Fitzgerald, Patrick; Wancewicz, Benjamin; Valdiviez, Luis; Wohlgemuth, Gert; Byram, Gregory; Choy, Ying Yng; Haffner, Bennett; Showalter, Megan R.; Vaniya, Arpana; Bloszies, Clayton S.; Folz, Jacob S.; Kind, Tobias; Flenniken, Ann M.; McKerlie, Colin; Nutter, Lauryl M.J.; Lloyd, Kent C.; Fiehn, Oliver.

In: Metabolites, Vol. 9, No. 5, 101, 01.05.2019.

Research output: Contribution to journal › Article › peer-review

Barupal, DK, Zhang, Y, Shen, T, Fan, S, Roberts, BS, Fitzgerald, P, Wancewicz, B, Valdiviez, L, Wohlgemuth, G, Byram, G, Choy, YY, Haffner, B, Showalter, MR, Vaniya, A, Bloszies, CS, Folz, JS, Kind, T, Flenniken, AM, McKerlie, C, Nutter, LMJ, Lloyd, KC & Fiehn, O 2019, 'A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium', Metabolites, vol. 9, no. 5, 101. https://doi.org/10.3390/metabo9050101

Barupal, Dinesh K. ; Zhang, Ying ; Shen, Tong ; Fan, Sili ; Roberts, Bryan S. ; Fitzgerald, Patrick ; Wancewicz, Benjamin ; Valdiviez, Luis ; Wohlgemuth, Gert ; Byram, Gregory ; Choy, Ying Yng ; Haffner, Bennett ; Showalter, Megan R. ; Vaniya, Arpana ; Bloszies, Clayton S. ; Folz, Jacob S. ; Kind, Tobias ; Flenniken, Ann M. ; McKerlie, Colin ; Nutter, Lauryl M.J. ; Lloyd, Kent C. ; Fiehn, Oliver. / A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium. In: Metabolites. 2019 ; Vol. 9, No. 5.

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abstract = "Mouse knockouts facilitate the study ofgene functions. Often, multiple abnormal phenotypes are induced when a gene is inactivated. The International Mouse Phenotyping Consortium (IMPC) has generated thousands of mouse knockouts and catalogued their phenotype data. We have acquired metabolomics data from 220 plasma samples from 30 unique mouse gene knockouts and corresponding wildtype mice from the IMPC. To acquire comprehensive metabolomics data, we have used liquid chromatography (LC) combined with mass spectrometry (MS) for detecting polar and lipophilic compounds in an untargeted approach. We have also used targeted methods to measure bile acids, steroids and oxylipins. In addition, we have used gas chromatography GC-TOFMS for measuring primary metabolites. The metabolomics dataset reports 832 unique structurally identified metabolites from 124 chemical classes as determined by ChemRICH software. The GCMS and LCMS raw data files, intermediate and finalized data matrices, R-Scripts, annotation databases, and extracted ion chromatograms are provided in this data descriptor. The dataset can be used for subsequent studies to link genetic variants with molecular mechanisms and phenotypes.",

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A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium

Abstract

Keywords

ASJC Scopus subject areas

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