Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA327058

Local Sample ID:	5_O_HFD
Subject ID:	SU003125
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

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Subject:

Subject ID:	SU003125
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
5_O_HFD	SA327058	FL038852	HFD	Diet
5_O_HFD	SA327058	FL038852	OligoMM	colonization

Collection:

Collection ID:	CO003118
Collection Summary:	Mice were euthanized with CO2 and colon was extracted.
Sample Type:	Colon

Treatment:

Treatment ID:	TR003134
Treatment Summary:	Germfree male C57BL/6N mice were associated with 0.2 ml of the freshly thawed microbial mixtures via oral gavage three times within one week at the age of five weeks. From week 8 onwards, diet was changed from autoclaved standard chow to synthetic control diet (CD) for two weeks. Thereafter, the mice were randomly assigned to four different groups fed the following diets for eight weeks (the references and main differences in composition between the diets are provided in Figure S1B): CD, control diet; CD-BA, control diet supplemented with the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) (each 0.1%); HFD, lard-based high-fat diet (48% energy from fat); HFD-BA, HFD supplemented with CA and CDCA. These diets were used due to the link between Coriobacteriia/E. lenta and bile acid metabolism as well as host metabolic health.

Treatment ID:

TR003134

Treatment Summary:

Germfree male C57BL/6N mice were associated with 0.2 ml of the freshly thawed microbial mixtures via oral gavage three times within one week at the age of five weeks. From week 8 onwards, diet was changed from autoclaved standard chow to synthetic control diet (CD) for two weeks. Thereafter, the mice were randomly assigned to four different groups fed the following diets for eight weeks (the references and main differences in composition between the diets are provided in Figure S1B): CD, control diet; CD-BA, control diet supplemented with the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) (each 0.1%); HFD, lard-based high-fat diet (48% energy from fat); HFD-BA, HFD supplemented with CA and CDCA. These diets were used due to the link between Coriobacteriia/E. lenta and bile acid metabolism as well as host metabolic health.

Sample Preparation:

Sampleprep ID:	SP003131
Sampleprep Summary:	Colon content was mixed with 5x ACN:H2O solvent and 4 steel beads for subsequent extraction in the bead mill. After centrifugation, 100 µL of the supernatant were mixed with 500 µL methanol:acetonitrile (ACN):water (2:3:1) followed by vortex and sonication. After centrifugation, 100 µL of the supernatant were dried in a SpeedVac™ vacuum concentrator (Eppendorf, Hamburg, Germany).

Combined analysis:

Analysis ID	AN004942	AN004943
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity II	Agilent 1290 Infinity II
Column	Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um)	Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6546 QTOF	Agilent 6546 QTOF
Ion Mode	NEGATIVE	POSITIVE
Units	Peak AUC	Peak AUC

Chromatography:

Chromatography ID:	CH003731
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um)
Column Temperature:	45
Flow Gradient:	0-5.5 min: 1% B; 5-20 min: 1-100% B; 20-22 min: 100% B; 22-22.5: 100-1% B; 22.5-25 min: 1% B
Flow Rate:	0.3 ml/min
Solvent A:	Water + 0.1% FA
Solvent B:	ACN + 0.1% FA
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004685
Analysis ID:	AN004942
Instrument Name:	Agilent 6546 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 50 – 1000 m/z. After each full scan, the 2 most intense ions were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.4, Waters Corporation) for further analysis.
Ion Mode:	NEGATIVE

MS ID:	MS004686
Analysis ID:	AN004943
Instrument Name:	Agilent 6546 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 50 – 1000 m/z. After each full scan, the 2 most intense ions were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.4, Waters Corporation) for further analysis.
Ion Mode:	POSITIVE