Summary of Study ST000879

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 PR000610. The data can be accessed directly via it's Project DOI: 10.21228/M8TH6S 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 IDST000879
Study TitleDiet, genetics and gut microbiome drive dynamic changes in plasma metabolites [plasma]
Study TypePlasma data
Study SummaryC57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2017-10-02
Num Groups12
Total Subjects47
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2018-01-29
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M8TH6S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN001429 AN001430 AN001431 AN001432
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Shimadzu Nexera X2 Waters Acquity Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2 mm) Phenomenex Luna NH2 (150 x 2.0mm) Waters Acquity BEH C18 (150 x 2.1mm, 1.7um) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Triple quadrupole Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap ABI Sciex 5500 QTrap Thermo Q Exactive Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE NEGATIVE POSITIVE
Units Peak area Peak area Peak area peak area

Chromatography:

Chromatography ID:CH001000
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2 mm)
Solvent A:10 mM ammonium formate and 0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH001001
Instrument Name:Waters Acquity
Column Name:Phenomenex Luna NH2 (150 x 2.0mm)
Solvent A:20 mM ammonium acetate and 20 mM ammonium hydroxide (Sigma-Aldrich) in water (VWR)
Solvent B:10 mM ammonium hydroxide in 75:25 v/v acetonitrile/methanol (VWR)
Chromatography Type:HILIC
  
Chromatography ID:CH001002
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C18 (150 x 2.1mm, 1.7um)
Solvent A:0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001003
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Solvent A:95:5:0.1 vol/vol/vol 10 mM ammonium acetate/methanol/acetic acid
Solvent B:99.9:0.1 vol/vol methanol/acetic acid
Chromatography Type:Reversed phase
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