Summary of Study ST001366

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 PR000934. The data can be accessed directly via it's Project DOI: 10.21228/M8ZH61 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	ST001366
Study Title	Malnutrition and Liver Metabolomics
Study Summary	RP-UPLC-FTMS (+/- ion detection) were conducted on hippocampi from healthy (CON) and malnourished (MAL) mice, and MAL-BG (malnutrition plus E.coli/Bacteroidales exposure) mice.
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	2020-04-24
Num Groups	3
Total Subjects	15
Num Females	15
Raw Data Available	Yes
Analysis Type Detail	LC-MS
Release Date	2021-06-30
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000934
Project DOI:	doi: 10.21228/M8ZH61
Project Title:	Malnutrition, Microbes, and Hippocampal Metabolomics
Project Summary:	Examining the role of malnutrition and gut microbes on CNS function using the MAL-BG murine model. RP-UPLC-FTMS was conducted on murine hippocampal tissue.
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
Contributors:	B. Brett Finlay

Subject:

Subject ID:	SU001440
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6J
Age Or Age Range:	7 weeks
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	Diet	Bacterial Exposure
SA099362	CON_1	CON	Healthy	No
SA099363	CON_2	CON	Healthy	No
SA099364	CON_5	CON	Healthy	No
SA099365	CON_3	CON	Healthy	No
SA099366	CON_4	CON	Healthy	No
SA099367	MALBG_3	MAL-BG	Malnourished	Yes
SA099368	MALBG_1	MAL-BG	Malnourished	Yes
SA099369	MALBG_2	MAL-BG	Malnourished	Yes
SA099370	MALBG_5	MAL-BG	Malnourished	Yes
SA099371	MALBG_4	MAL-BG	Malnourished	Yes
SA099372	MAL_3	MAL	Malnourished	No
SA099373	MAL_1	MAL	Malnourished	No
SA099374	MAL_2	MAL	Malnourished	No
SA099375	MAL_4	MAL	Malnourished	No
SA099376	MAL_5	MAL	Malnourished	No

Showing results 1 to 15 of 15

Showing results 1 to 15 of 15

Collection:

Collection ID:	CO001435
Collection Summary:	Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.
Sample Type:	Hippocampus

Treatment:

Treatment ID:	TR001455
Treatment Summary:	CON = control mice on healthy diet, MAL = mice placed on a protein/fat deficient diet (malnourished), MAL-BG = MAL mice plus iterative E.coli/Bacteroidales exposure

Sample Preparation:

Sampleprep ID:	SP001448
Sampleprep Summary:	Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. 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. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively.

Sampleprep ID:

SP001448

Sampleprep Summary:

Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. 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. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively.

Combined analysis:

Analysis ID	AN002273	AN002274
Chromatography ID	CH001672	CH001672
MS ID	MS002117	MS002118
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Waters BEH C8 (50 x 2.1mm,1.7um)	Waters BEH C8 (50 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo LTQ-Orbitrap Velos Pro	Thermo LTQ-Orbitrap Velos Pro
Ion Mode	POSITIVE	NEGATIVE
Units	abundance	abundance

Chromatography:

Chromatography ID:	CH001672
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters BEH C8 (50 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002117
Analysis ID:	AN002273
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods).
Ion Mode:	POSITIVE

MS ID:	MS002118
Analysis ID:	AN002274
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods).
Ion Mode:	NEGATIVE