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.

Study ID	ST001959
Study Title	Investigation of serum metabolites in the AMPK intestinal KO mice
Study Summary	Conducted 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
Department	Diabetes Complications & Metabolism
Last Name	Zhang
First Name	Eryun
Address	1500 Duarte Rd, Duarte, CA91010
Email	zhangey0220@126.com
Phone	16268735517
Submit Date	2021-10-27
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-01-08
Release Version	1

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
SA184600	A329pos	AMPKfl/fl(control) mice	HFD
SA184601	A330pos	AMPKfl/fl(control) mice	HFD
SA184602	A331pos	AMPKfl/fl(control) mice	HFD
SA184603	A328pos	AMPKfl/fl(control) mice	HFD
SA184596	B334pos	AMPK intestinal KO mice	HFD
SA184597	B335pos	AMPK intestinal KO mice	HFD
SA184598	B333pos	AMPK intestinal KO mice	HFD
SA184599	B332pos	AMPK intestinal KO mice	HFD

Showing results 1 to 8 of 8

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.

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.

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	HILIC
Chromatography system	Agilent 1290 Infinity
Column	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Triple TOF
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:	HILIC

MS:

MS ID:	MS002972
Analysis ID:	AN003194
Instrument Name:	ABI Sciex 5600 TripleTOF
Instrument Type:	Triple TOF
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