Summary of study ST000930

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 PR000644. The data can be accessed directly via it's Project DOI: 10.21228/M8F380 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000930
Study TitleDefine alterations in the gut metabolome of mice infected with C. difficile
Study TypeTime course experiment
Study SummaryC57BL/6 mice were treated with antibiotics to make them susceptible to C. difficile. Mice were challenged with C. difficile and the infection was monitored for 30 hours post challenge. Mice were sacrificed at 0 hr, 12 hr, 24 hr, and 30 hr post challenge with C. difficile and gut content was collected for untargeted metabolomic analysis. The aim of this project was to define the gut metabolome throughout C. difficile infection.
Institute
North Carolina State University
DepartmentPHP
LaboratoryTheriot
Last NameTheriot
First NameCasey
Address1051 William Moore Drive
Emailcmtherio@ncsu.edu
Phone919-513-0711
Submit Date2018-02-26
Num Groups4
Total Subjects31
Num Males16
Num Females15
Analysis Type DetailLC-MS
Release Date2018-03-15
Release Version1
Casey Theriot Casey Theriot
https://dx.doi.org/10.21228/M8F380
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000644
Project DOI:doi: 10.21228/M8F380
Project Title:Alterations in the gut metabolome throughout C. difficile infection
Project Summary:C57BL/6 mice were treated with antibiotics to make them susceptible to C. difficile. Mice were challenged with C. difficile and the infection was monitored for 30 hours post challenge. Mice were sacrificed at 12 hr, 24 hr, and 30 hr post challenge with C. difficile and gut content was collected for untargeted metabolomic analysis. The aim of this project was to define the gut metabolome throughout C. difficile infection.
Institute:North Carolina State University
Department:Population Health and Pathobiology
Laboratory:Theriot
Last Name:Theriot
First Name:Casey
Address:1051 William Moore Drive, Raleigh, NC, 27607, USA
Email:cmtherio@ncsu.edu
Phone:9195130711
Funding Source:NIGMS K01 and R35

Subject:

Subject ID:SU000969
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:5-8
Gender:Male and female
Animal Light Cycle:12 hr cycle of light and darkness

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Hours
SA055499CD_0hr_8-
SA055500CD_0hr_2-
SA055501CD_0hr_6-
SA055502CD_0hr_7-
SA055503CD_0hr_3-
SA055504CD_0hr_4-
SA055505CD_0hr_5-
SA055506CD_12hr_712
SA055507CD_12hr_812
SA055508CD_12hr_612
SA055509CD_12hr_312
SA055510CD_12hr_112
SA055511CD_12hr_512
SA055512CD_12hr_212
SA055513CD_12hr_412
SA055514CD_24hr_724
SA055515CD_24hr_824
SA055516CD_24hr_624
SA055517CD_24hr_124
SA055518CD_24hr_524
SA055519CD_24hr_324
SA055520CD_24hr_224
SA055521CD_24hr_424
SA055522CD_30hr_730
SA055523CD_30hr_830
SA055524CD_30hr_630
SA055525CD_30hr_330
SA055526CD_30hr_130
SA055527CD_30hr_230
SA055528CD_30hr_430
SA055529CD_30hr_530
Showing results 1 to 31 of 31

Collection:

Collection ID:CO000963
Collection Summary:Cecal content was collected from mice at the time of necropsy and flash frozen in liquid nitrogen until later metabolomics analysis.
Sample Type:Cecum
Storage Conditions:-80℃

Treatment:

Treatment ID:TR000983
Treatment Summary:Mice were treated with cefoperazone in their drinking water for 5 days with a two day washout before being challenged with C. difficile spores. Mice were euthanized at time 0hr, prior to C. difficile challenge, and post challenge at 12, 24, and 30 hr. The cecum of mice was collected, flash frozen and stored in the -80C until processing.

Sample Preparation:

Sampleprep ID:SP000976
Sampleprep Summary:Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.

Combined analysis:

Analysis ID AN001524
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Waters Acquity BEH C8 (100 x 2mm, 1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units scaled intensity

Chromatography:

Chromatography ID:CH001074
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C8 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS001404
Analysis ID:AN001524
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:UNSPECIFIED
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