Summary of Study ST001367

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 PR000935. The data can be accessed directly via it's Project DOI: 10.21228/M8TT3R 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 ID	ST001367
Study Title	Malnutrition and Liver Metabolomics Pre-Intervention (part-I)
Study Summary	RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished (MAL) mice. To examine the impact of gut microbes and malnutrition, data was also collected from a third group (MBG).
Institute	University of British Columbia
Department	Microbiology and Immunology
Laboratory	B. Brett Finlay
Last Name	Bauer
First Name	Kylynda
Address	Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Email	kcbauer@msl.ubc.ca
Phone	(604) 822-2210
Submit Date	2020-04-20
Num Groups	3
Total Subjects	12
Num Females	12
Analysis Type Detail	LC-MS
Release Date	2020-08-03
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000935
Project DOI:	doi: 10.21228/M8TT3R
Project Title:	Malnutrition Gut microbes and Liver Metabolomics
Project Summary:	Examining the role of malnutrition and gut microbes on fatty liver using the MAL-BG murine model. RP-UPLC-FTMS and HILIC-FTMS were conducted on murine livers prior and following dietary intervention. This submission contains prior intervention raw data.
Institute:	University of British Columbia
Department:	Microbiology and Immunology
Laboratory:	Finlay
Last Name:	Bauer
First Name:	Kylynda
Address:	#301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Email:	kcbauer@msl.ubc.ca
Phone:	(604) 822-2210
Project Comments:	Pre-Intervention
Contributors:	B. Brett Finlay

Subject:

Subject ID:	SU001441
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6J
Age Or Age Range:	~7 weeks (Pre-intervention)
Gender:	Female
Animal Animal Supplier:	Jackson Laboratories
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Treatment	Start Diet	Final Diet
SA099377	CONA_4	CON	Healthy	Healthy
SA099378	CONA_3	CON	Healthy	Healthy
SA099379	CONA_1	CON	Healthy	Healthy
SA099380	CONA_2	CON	Healthy	Healthy
SA099381	MALA_4	MAL	Malnourished	Malnourished
SA099382	MALA_3	MAL	Malnourished	Malnourished
SA099383	MALA_2	MAL	Malnourished	Malnourished
SA099384	MALA_1	MAL	Malnourished	Malnourished
SA099385	MBGA_4	MBG	Malnourished	Malnourished
SA099386	MBGA_2	MBG	Malnourished	Malnourished
SA099387	MBGA_1	MBG	Malnourished	Malnourished
SA099388	MBGA_3	MBG	Malnourished	Malnourished

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001436
Collection Summary:	Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.
Sample Type:	Liver

Treatment:

Treatment ID:	TR001456
Treatment Summary:	CON = control mice placed on a healthy (standard mouse chow), MAL = mice placed on an isocaloric malnourished diet (protein/fat deficient), MBG = MAL mice with repeated exposure to fecal microbes, mice were placed on the respective treatments for one month following weaning.

Sample Preparation:

Sampleprep ID:	SP001449
Sampleprep Summary:	RP-UPLC-FTMS: Individual mouse liver samples were mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added to an Eppendorf tube. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase RP-UPLC-FTMS. HILIC-FTMS: Individual sample supernatants were mixed with 120 μL of water, 180 μL of methanol and 195 μL of chloroform. The mixture was vortex mixed at 3000 rpm for 30 s before centrifugal clarification. 300 μL of the upper, aqueous phase was precisely taken out and transferred to a “V”-shape LC injection microvial and was dried down under a gentle nitrogen gas flow in the nitrogen evaporator. The residue was reconstituted in 50 μL of 80% acetonitrile. 10 μL was injected for HILIC-FTMS. *See Methods

Sampleprep ID:

SP001449

Sampleprep Summary:

RP-UPLC-FTMS: Individual mouse liver samples were mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added to an Eppendorf tube. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase RP-UPLC-FTMS. HILIC-FTMS: Individual sample supernatants were mixed with 120 μL of water, 180 μL of methanol and 195 μL of chloroform. The mixture was vortex mixed at 3000 rpm for 30 s before centrifugal clarification. 300 μL of the upper, aqueous phase was precisely taken out and transferred to a “V”-shape LC injection microvial and was dried down under a gentle nitrogen gas flow in the nitrogen evaporator. The residue was reconstituted in 50 μL of 80% acetonitrile. 10 μL was injected for HILIC-FTMS. *See Methods

Chromatography:

Chromatography ID:	CH001673
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters BEH C8 (50 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH001674
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters HILIC (100 x 2.1mm,1.8um)
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN002275
Analysis Type:	MS
Chromatography ID:	CH001673
Num Factors:	3
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST001367_AN002275_Results.txt
Units:	Abundance

Analysis ID:	AN002276
Analysis Type:	MS
Chromatography ID:	CH001673
Num Factors:	3
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST001367_AN002276_Results.txt
Units:	abundance

Analysis ID:	AN002277
Analysis Type:	MS
Chromatography ID:	CH001674
Num Factors:	3
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST001367_AN002277_Results.txt
Units:	Abundance

Analysis ID:	AN002278
Analysis Type:	MS
Chromatography ID:	CH001674
Num Factors:	3
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST001367_AN002278_Results.txt
Units:	abundance