Summary of Study ST000028

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 PR000025. The data can be accessed directly via it's Project DOI: 10.21228/M8201W This work is supported by NIH grant, U2C- DK119886.

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Study IDST000028
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Urine)
Study TypeMetabolomics
Study SummaryIn the DuraSTAT sub-study, a total of 18 samples from 8 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a high fat diet.
Institute
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2014-03-14
Num Groups2
Total Subjects6
Study CommentsDuraSTAT_Urine
Raw Data AvailableYes
Uploaded File Size400K approx
Analysis Type DetailNMR
Release Date2015-03-14
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8201W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000025
Project DOI:doi: 10.21228/M8201W
Project Title:Metabolomics Involved in Early Life Antibiotic Exposures
Project Type:Obesity modeling of antibiotic exposure
Project Summary:The project Metabolomics Involved in Early Life Antibiotic Exposures profiled a total of 90 samples from five sub-studies (DuraSTAT, TranSTAT, NOD, EstroSTAT and VG STAT) which included a total of four sample matrices (urine, serum, liver tissue and cecal contents). Within each sub-study, there were three sample matrices except for VG STAT, for which there was only two. For each matrix type within each sub-study 6 samples were analyzed for a total of 18 samples per sub-study (9 of each in VG STAT), the samples were equally divided into STAT/PAT-treated (sub-therapeutic antibiotic treatment (STAT) and therapeutic dose-pulsed antibiotic treatment (PAT)) collected at various time-points versus untreated Controls for each matrix.
Institute:New York University
Department:School of Medicine
Laboratory:Blaser Laboratory
Last Name:Blaser
First Name:Martin
Address:550 First Avenue, BCD 690, New York, NY 10016
Email:Martin.Blaser@nyumc.org
Publications:Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nature Reviews. Genetics 2012; 13; 260-270

Subject:

Subject ID:SU000045
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:8 weeks at collection
Gender:Female
Animal Animal Supplier:Jackson Labs
Animal Housing:Conventional
Animal Feed:High Fat Diet
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Treatment Group
SA001622UDC029Control
SA001623UDC032Control
SA001624UDC030Control
SA001625UPL102Pool QC
SA001626UPL103Pool QC
SA001627UPL101Pool QC
SA001628UDS052STAT
SA001629UDS039STAT
SA001630UDS054STAT
Showing results 1 to 9 of 9

Collection:

Collection ID:CO000028
Sample Type:urine
Collection Time:8 weeks

Treatment:

Treatment ID:TR000046
Treatment Summary:Three mice were given STAT penicillin and 3 mice were non-treated controls. STAT = sub-therapeutic antibiotic treatment.
Treatment Compound:STAT penicillin

Sample Preparation:

Sampleprep ID:SP000041
Sampleprep Summary:Frozen urine study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 400 µL were transferred into BSI-labeled eppendorf tubes. Aliquots of 100 µL per study sample were also transferred into a 10 mL tube to generate pooled samples for QC during analysis, and 400 µL was transferred into BSI-labeled eppendorf tubes. D2O (230 µL) was added to each tube. Chenomx Internal Standard solution (Chenomx ISTD, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) was added (70 µl) to the tubes. Tubes were vortexed for 30 seconds and centrifuged at 12000 rcf for 5min. A 600 µL aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition.
Sampleprep Protocol Filename:DuraSTAT_Urine_Metabolomics_Procedure.docx

Chromatography:

Chromatography ID:CH000029

Analysis:

Analysis ID:AN000048
Laboratory Name:RTI/ DHHMRI
Analysis Type:NMR
Analysis Comments:NMR (700 MHz)
Acquisition Date:41522
Software Version:Top Spin 3.2
Operator Name:Wimal Pathmasiri/ Kevin Knagge/ Jason Winnikie
Randomization Order:yes
Detector Type:NMR
Data Format:NMR
Chromatography ID:CH000029
Num Factors:3

NMR:

NMR ID:NM000010
Analysis ID:AN000048
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5mM
Spectrometer Frequency:700 MHz
NMR Probe:cyrogenically cooled ATMA inverse probe
NMR Solvent:D2O
NMR Tube Size:5mm x 4inch
Shimming Method:topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:14.84 us
Power Level:25.704w
Receiver Gain:4
Offset Frequency:3293.10 Hz
Chemical Shift Ref Cpd:DSS
Temperature:298.1 K
Number Of Scans:64
Dummy Scans:4
Acquisition Time:2.3243434
Relaxation Delay:2 s
Spectral Width:20.1358
Num Data Points Acquired:65536
Real Data Points:65536
Line Broadening:0.5
Zero Filling:yes
Apodization:lorentzian
Baseline Correction Method:polynomial
Chemical Shift Ref Std:DSS
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