Summary of Study ST002275

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 PR001456. The data can be accessed directly via it's Project DOI: 10.21228/M8HQ5P 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	ST002275
Study Title	Insights from hippocampal neurogenesis and brain tumor development in a mouse model of experimental colitis induced by dextran sodium sulfate
Study Summary	We here reported investigations on a model of chemically induced experimental colitis by oral administration of sodium dextran sulfate (DSS) in C57BL/6 mice. We investigated, in vivo, the crosstalk between the intestine and the brain, evaluating the consequences of intestinal inflamma-tion on neuroinflammation and hippocampal adult neurogenesis. By using different DSS admin-istration strategies, we were able to induce acute or chronic colitis simulating clinical character-istics observed in IBD patients
Institute	Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile
Last Name	Lorenzo Rebenaque
First Name	Laura
Address	calle seminari sn Alfara del Patriarca
Email	laura.lorenzorebenaque@uchceu.es
Phone	615056012
Submit Date	2022-08-30
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-09-16
Release Version	1

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Project:

Project ID:	PR001456
Project DOI:	doi: 10.21228/M8HQ5P
Project Title:	Gut-brain axis: Insights from hippocampal neurogenesis and brain tumor development in a mouse model of experimental colitis induced by dextran sodium sulfate
Project Summary:	We here reported investigations on a model of chemically induced experimental colitis by oral administration of sodium dextran sulfate (DSS) in C57BL/6 mice. We investigated, in vivo, the crosstalk between the intestine and the brain, evaluating the consequences of intestinal inflamma-tion on neuroinflammation and hippocampal adult neurogenesis. By using different DSS admin-istration strategies, we were able to induce acute or chronic colitis simulating clinical character-istics observed in IBD patients
Institute:	Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile
Last Name:	Lorenzo Rebenaque
First Name:	Laura
Address:	calle seminari sn Alfara del Patriarca
Email:	laura.lorenzorebenaque@uchceu.es
Phone:	615056012

Subject:

Subject ID:	SU002361
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	Group	Moment
SA217842	DSS A WK2 2	DSS	14 ACUTE
SA217843	DSS A WK2 3	DSS	14 ACUTE
SA217844	DSS A WK2 4	DSS	14 ACUTE
SA217845	DSS A WK2 1	DSS	14 ACUTE
SA217846	DSS A WK2 5	DSS	14 ACUTE
SA217847	DSS A WK1 1	DSS	7 ACUTE
SA217848	DSS A WK1 2	DSS	7 ACUTE
SA217849	DSS A WK1 5	DSS	7 ACUTE
SA217850	DSS A WK1 3	DSS	7 ACUTE
SA217851	DSS A WK1 4	DSS	7 ACUTE
SA217852	DSS C5	DSS	CRONICA
SA217853	DSS C8	DSS	CRONICA
SA217854	DSS C7	DSS	CRONICA
SA217855	DSS C4	DSS	CRONICA
SA217856	DSS C2	DSS	CRONICA
SA217857	DSS C3	DSS	CRONICA
SA217858	DSS C6	DSS	CRONICA
SA217859	DSS C1	DSS	CRONICA
SA217860	UN A WK2 1	UN	14 ACUTE
SA217861	UN A WK2 2	UN	14 ACUTE
SA217862	UN A WK1 3	UN	7 ACUTE
SA217863	UN A WK1 5	UN	7 ACUTE
SA217864	UN A WK1 4	UN	7 ACUTE
SA217865	UN A WK1 1	UN	7 ACUTE
SA217866	UN A WK1 2	UN	7 ACUTE
SA217867	UN C 3	UN	CRONICA
SA217868	UN C 2	UN	CRONICA
SA217869	UN C 1	UN	CRONICA
SA217870	UN C 4	UN	CRONICA
SA217871	UN C 5	UN	CRONICA
SA217872	UN C 6	UN	CRONICA
SA217873	UN C 7	UN	CRONICA

Showing results 1 to 32 of 32

Showing results 1 to 32 of 32

Collection:

Collection ID:	CO002354
Collection Summary:	Fecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment
Sample Type:	Colon

Treatment:

Treatment ID:	TR002373
Treatment Summary:	For induction of acute colitis, male mice of 8 weeks of age were administered with a single cycle of 0.7% (w/v) DSS for 7 days followed by 3 or 7 days of DSS-free drinking water. For induction of chronic colitis, male mice of 8 weeks of age were treated with 3 repeated DSS cycles of 7 days each followed by a recovery period of 14 days with DSS-free drinking water.

Sample Preparation:

Sampleprep ID:	SP002367
Sampleprep Summary:	A pool of 2 frozen stool samples from 2 independent mice (total dry weigh 15-25mg) from the different experimental groups [UN-Acute n=5; UN-Chronic n= 7; DSS-acute, at the end (n=5) or one week after DSS treatment (n=5) and DSS-chronic (n=8)] were mixed and shacked for two times in 750 l of aqueous solution with 75% of methanol, 0.1% of formic acid and 1ug/ml of formonetin as internal control for 20 min at room temperature. The mixture was then vortexed for 3 min followed by centrifugation at 15 000g for 15 min. The suspension (600μL) was used for metabolic profiling. For the LC-ESI-MS analysis, samples were transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. Liquid chromatography coupled to high-resolution mass spectrometry conditions were as pre-viously reported https://www.mdpi.com/1422-0067/22/18/9716.

Sampleprep ID:

SP002367

Sampleprep Summary:

A pool of 2 frozen stool samples from 2 independent mice (total dry weigh 15-25mg) from the different experimental groups [UN-Acute n=5; UN-Chronic n= 7; DSS-acute, at the end (n=5) or one week after DSS treatment (n=5) and DSS-chronic (n=8)] were mixed and shacked for two times in 750 l of aqueous solution with 75% of methanol, 0.1% of formic acid and 1ug/ml of formonetin as internal control for 20 min at room temperature. The mixture was then vortexed for 3 min followed by centrifugation at 15 000g for 15 min. The suspension (600μL) was used for metabolic profiling. For the LC-ESI-MS analysis, samples were transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. Liquid chromatography coupled to high-resolution mass spectrometry conditions were as pre-viously reported https://www.mdpi.com/1422-0067/22/18/9716.

Combined analysis:

Analysis ID	AN003717	AN003718
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate	Thermo Dionex Ultimate
Column	Phenomenex Luna (100 x 2.1mm,2.5um)	Phenomenex Luna (100 x 2.1mm,2.5um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	m/z ratio	m/z ratio

Chromatography:

Chromatography ID:	CH002754
Instrument Name:	Thermo Dionex Ultimate
Column Name:	Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003466
Analysis ID:	AN003717
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	ESI/APCI. Untargeted metabolomics was performed using the Compound Discovered software (Thermofisher Scientific), which performs chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).
Ion Mode:	POSITIVE

MS ID:	MS003467
Analysis ID:	AN003718
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	ESI/APCI. Untargeted metabolomics was performed using the Compound Discovered software (Thermofisher Scientific), which performs chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).
Ion Mode:	NEGATIVE