Summary of study ST001959

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001246. The data can be accessed directly via it's Project DOI: 10.21228/M8NM5W This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001959
Study TitleInvestigation of serum metabolites in the AMPK intestinal KO mice
Study SummaryConducted serum untargeted metabolomics analysis in AMP-activated protein kinase (AMPK) intestinal KO mice and control mice under high-fat diet (HFD) conditions
Institute
City of Hope National Medical Center
DepartmentDiabetes Complications & Metabolism
Last NameZhang
First NameEryun
Address1500 Duarte Rd, Duarte, CA91010
Emailzhangey0220@126.com
Phone16268735517
Submit Date2021-10-27
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2022-01-08
Release Version1
Eryun Zhang Eryun Zhang
https://dx.doi.org/10.21228/M8NM5W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001246
Project DOI:doi: 10.21228/M8NM5W
Project Title:Serum metabolomics study in intestinal AMPK KO mice
Project Type:Serum untargeted metabolomics
Project Summary:Serum untargeted metabolomics studies on serum samples from intestinal AMPK KO mice and control mice
Institute:City of Hope National Medical Center
Department:Diabetes Complications & Metabolism
Last Name:Zhang
First Name:Eryun
Address:1500 Duarte Rd, Duarte, CA, 91010, USA
Email:erzhang@coh.org
Phone:6268735517

Subject:

Subject ID:SU002039
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment
SA184600A329posAMPKfl/fl(control) mice HFD
SA184601A330posAMPKfl/fl(control) mice HFD
SA184602A331posAMPKfl/fl(control) mice HFD
SA184603A328posAMPKfl/fl(control) mice HFD
SA184596B334posAMPK intestinal KO mice HFD
SA184597B335posAMPK intestinal KO mice HFD
SA184598B333posAMPK intestinal KO mice HFD
SA184599B332posAMPK intestinal KO mice HFD
Showing results 1 to 8 of 8

Collection:

Collection ID:CO002032
Collection Summary:Collect whole blood in a covered test tube,leave the tube in a standing position and wait 30 min.Centrifuge 1500 g 10 min at 4ºC.Take out the serum.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002051
Treatment Summary:C57BL/6-AMPKa1flox/flox mice (#014141), and B6.Cg-Tg (Vil-cre) 1000Gum/J (#021504) were purchased from Jackson Laboratory (Bar Harbor, ME). AMPK intestinal KO (AMPK-IKO) mice were generated by cross-breeding C57BL/6-AMPKa1flox/flox mice with B6.Cg-Tg (Vil-cre) 1000Gum/J. All animal procedures were approved by the City of Hope Institutional Animal Care and Use Committee and conducted in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals. 6-week-old male mice were housed in a temperature (22-23°C) and light-controlled vivarium with free access to water and high-fat diet (HFD, 60% kcal fat; D12492, Research Diets, New Brunswick, NJ) for 12 weeks.

Sample Preparation:

Sampleprep ID:SP002045
Sampleprep Summary:50 µL of serum was used for metabolites extraction. 200 μL extract solution (acetonitrile: methanol = 1: 1) containing isotopically labeled internal standard mixture was added to each sample. After vortexing for 1 min, the samples were sonicated for 10 min in cold water bath. Then, the samples were incubated at -40 °C for 1 h, and centrifuged at 12000 rpm for 15 min at 4°C. 200 µL of supernatant were transferred to a fresh tube, and dried in a vacuum concentrator at 37 °C. Then, the dried samples were reconstituted in 200 µL of 50% acetonitrile by sonication on ice for 10 min. The constitution was then centrifuged at 13000 rpm for 15 min at 4°C, and 75 µL of supernatant were transferred to a fresh glass vial for LC/MS analysis.

Combined analysis:

Analysis ID AN003194
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name ABI Sciex 5600 TripleTOF
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH002362
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002972
Analysis ID:AN003194
Instrument Name:ABI Sciex 5600 TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:UHPLC-MS raw data files were converted into mzXML format using the “msconvert” program from Pro-teoWizard and then analyzed by the XCMS 67 and CAMERA toolbox 68 with R statistical software. The CentWave algorithm in XCMS was used for peak detection. The parameter “peak-width” was set as (5, 20) in units of seconds, referring to the minimum and maximum peak widths for peak detection. The pa-rameter ‘‘snthresh’’ is set as 3 for sensitive peak detection. For multiple UHPLC–MS data files, an or-dered bijective interpolated warping (OBI-Warp) algorithm in XCMS was used for peak alignment.
Ion Mode:POSITIVE
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