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

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
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