A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-05-01
|
| Series: | Metabolites |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-1989/9/5/101 |
| _version_ | 1818251719780335616 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Dinesh K. Barupal |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T16:12:45Z |
| format | Article |
| id | doaj.art-82bd7caeac484fafbefa4cf0cc55a23b |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-12-12T16:12:45Z |
| publishDate | 2019-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-82bd7caeac484fafbefa4cf0cc55a23b2022-12-22T00:19:10ZengMDPI AGMetabolites2218-19892019-05-019510110.3390/metabo9050101metabo9050101A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping ConsortiumDinesh K. Barupal0Ying Zhang1Tong Shen2Sili Fan3Bryan S. Roberts4Patrick Fitzgerald5Benjamin Wancewicz6Luis Valdiviez7Gert Wohlgemuth8Gregory Byram9Ying Yng Choy10Bennett Haffner11Megan R. Showalter12Arpana Vaniya13Clayton S. Bloszies14Jacob S. Folz15Tobias Kind16Ann M. Flenniken17Colin McKerlie18Lauryl M. J. Nutter19Kent C. Lloyd20Oliver Fiehn21NIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USAThe Centre for Phenogenomics, Toronto, ON M5T 3H7, CanadaThe Centre for Phenogenomics, Toronto, ON M5T 3H7, CanadaThe Centre for Phenogenomics, Toronto, ON M5T 3H7, CanadaMouse Biology Program, University of California, Davis, Davis, CA 95616, USANIH-West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USAMouse 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.https://www.mdpi.com/2218-1989/9/5/101Metabolic phenotypingmetabolomicslipidomicsfunctional genomicsmouse knockoutsIMPCLC-MSGC-MS |
| spellingShingle | 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 A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium Metabolites Metabolic phenotyping metabolomics lipidomics functional genomics mouse knockouts IMPC LC-MS GC-MS |
| title | A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium |
| title_full | A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium |
| title_fullStr | A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium |
| title_full_unstemmed | A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium |
| title_short | A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium |
| title_sort | comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium |
| topic | Metabolic phenotyping metabolomics lipidomics functional genomics mouse knockouts IMPC LC-MS GC-MS |
| url | https://www.mdpi.com/2218-1989/9/5/101 |
| work_keys_str_mv | AT dineshkbarupal acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT yingzhang acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT tongshen acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT silifan acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT bryansroberts acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT patrickfitzgerald acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT benjaminwancewicz acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT luisvaldiviez acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT gertwohlgemuth acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT gregorybyram acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT yingyngchoy acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT bennetthaffner acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT meganrshowalter acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT arpanavaniya acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT claytonsbloszies acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT jacobsfolz acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT tobiaskind acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT annmflenniken acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT colinmckerlie acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT laurylmjnutter acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT kentclloyd acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT oliverfiehn acomprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT dineshkbarupal comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT yingzhang comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT tongshen comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT silifan comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT bryansroberts comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT patrickfitzgerald comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT benjaminwancewicz comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT luisvaldiviez comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT gertwohlgemuth comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT gregorybyram comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT yingyngchoy comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT bennetthaffner comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT meganrshowalter comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT arpanavaniya comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT claytonsbloszies comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT jacobsfolz comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT tobiaskind comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT annmflenniken comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT colinmckerlie comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT laurylmjnutter comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT kentclloyd comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium AT oliverfiehn comprehensiveplasmametabolomicsdatasetforacohortofmouseknockoutswithintheinternationalmousephenotypingconsortium |