Summary of study ST000031

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 IDST000031
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(TranSTAT-Serum)
Study TypeMetabolomics
Study SummaryIn the TranSTAT sub-study, a total of 18 samples from 8 week old, female Swiss webster mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were inoculated with cecal contents from STAT mice and 3 mice/matrix were inoculated with cecal contents from Control mice. 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 CommentsTranSTAT_Serum Study
Raw Data AvailableYes
Raw Data File Type(s).txt,binary files, .par
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

Select appropriate tab below to view additional metadata details:


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:SU000048
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Swiss Webster Mice
Gender:Female
Animal Animal Supplier:Taconic
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
SA001655STC001Control
SA001656STC005Control
SA001657STC003Control
SA001658SPL202Pooled QC
SA001659SPL203Pooled QC
SA001660SPL201Pooled QC
SA001661STS005STAT
SA001662STS002STAT
SA001663STS008STAT
Showing results 1 to 9 of 9

Collection:

Collection ID:CO000031
Sample Type:blood
Collection Time:8 weeks
Blood Serum Or Plasma:serum

Treatment:

Treatment ID:TR000049
Treatment Summary:Three mice were inoculated with cecal contents from STAT mice and 3 mice were inoculated with cecal contents from control mice. STAT = sub-therapeutic antibiotic treatment.
Treatment Route:cecal transfer

Sample Preparation:

Sampleprep ID:SP000044
Sampleprep Summary:Frozen serum study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 50/100 µL (sub-study dependent) were transferred into BSI-labeled eppendorf tubes. Purchased mouse sera (Sigma #S7273) was also transferred into three BSI-labeled eppendorf tubes (50/100 µL) for QC samples during analysis. Freshly prepared 0.9% Saline (wt/v) solution in 10% D2O, was added to each tube (150/100 µL) and they were vortexed for 30 seconds. Freshly prepared 10 mM Formate solution containing 2% (wt/v) NaN3 was added to each tube (50 µL) to serve as internal standard and they were vortexed for 30 seconds again, then centrifuged at 12000 rcf for 5 minutes at 4 °C. A 200 µL aliquot of the supernatant was transferred into 3 mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition.
Sampleprep Protocol Filename:TranSTAT_Serum_Metabolomics_Procedure.docx

Chromatography:

Chromatography ID:CH000032

Analysis:

Analysis ID:AN000051
Laboratory Name:RTI/ DHHMRI
Analysis Type:NMR
Analysis Comments:NMR (700 MHz)
Acquisition Date:41527
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:CH000032
Num Factors:3

NMR:

NMR ID:NM000013
Analysis ID:AN000051
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:Deuterium
Standard Concentration:1.0 mM
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:cpmgpr1d
Water Suppression:presat
Pulse Width:14.84 us
Power Level:25.704w
Receiver Gain:4.5
Offset Frequency:3300.70 Hz
Chemical Shift Ref Cpd:Formate
Temperature:298.1 K
Number Of Scans:512
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:Formate
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