Summary of Study ST000039

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 IDST000039
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(VGSTAT-Liver)
Study TypeMetabolomics
Study SummaryIn the VG STAT sub-study, a total of 18 samples from 7 week old, male C57BL/6 mice; comprised of 9 cecal content samples and 9 liver tissue samples were analyzed. Three mice/matrix were given penicillin VK, 3 were given penicillin G, and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a normal 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 CommentsVG STAT_Liver Study
Raw Data AvailableYes
Uploaded File Size464 K
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:SU000056
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:7 weeks at collection
Gender:Male
Animal Animal Supplier:Jackson Labs
Animal Housing:conventional bedding
Animal Feed:normal 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
SA001745LVC018Control
SA001746LVC023Control
SA001747LVC020Control
SA001748LPL202Pool QC
SA001749LPL203Pool QC
SA001750LPL102Pool QC
SA001751LPL103Pool QC
SA001752LPL101Pool QC
SA001753LPL201Pool QC
SA001754LVG065STAT (pen G)
SA001755LVG059STAT (pen G)
SA001756LVG061STAT (pen G)
SA001757LVV039STAT (pen V)
SA001758LVV036STAT (pen V)
SA001759LVV040STAT (pen V)
Showing results 1 to 15 of 15

Collection:

Collection ID:CO000039
Sample Type:liver
Collection Time:7 weeks

Treatment:

Treatment ID:TR000057
Treatment Summary:Three mice were given penicillin VK, three were given penicillin G, and 3 mice matrix were non-treated controls. STAT = sub-therapeutic antibiotic treatment.
Treatment Compound:Penicillin VK and Penicillin G

Sample Preparation:

Sampleprep ID:SP000052
Sampleprep Summary:Frozen liver samples were weighed (50-100 mg) into labeled homogenizer bead tubes. Cold acetonitrile:water (50%) was added to tissue based on weight to make 1 mg/mL homogenates. The samples were extracted and homogenized on a Spex Geno/Grinder for two 45 second pulses at 1750 rpm. Samples were centrifuged at 12000 rcf for 5 min. Liver supernatants were transferred into BSI-labeled tubes. A 500 μL aliquot/sample was transferred into a second set of BSI-labeled tubes for further processing. To make pooled samples, a 300 μL aliquot of selected TranSTAT liver supernatants was combined in a 2 mL tube and used for QC samples in DuraSTAT, TranSTAT, EstroSTAT and NOD sub-studies. Additionally, a 200 μL aliquot of selected VG STAT liver supernatants was combined in a separate 2 mL tube and used as QC samples in the VG STAT sub-study. Three 500 μL aliquots were transferred into BSI-labeled tubes for each set of Pooled QC samples. All samples were then dried on an Eppendorf rotaVap (V-AL setting) at 30°C until dry and stored at -80 °C. On the second day of processing, 630 μL of D2O was added into each dried liver extract 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), and the samples were vortexed on a multi-tube vortexer for 10 minutes at speed 5. Tubes were then centrifuged at 12000 rcf for 5 minutes and a 600 μL aliquot of the supernatant was transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition.
Sampleprep Protocol Filename:VG_STAT_Liver_Metabolomics_Procedure.docx

Chromatography:

Chromatography ID:CH000040

Analysis:

Analysis ID:AN000059
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:CH000040
Num Factors:4

NMR:

NMR ID:NM000021
Analysis ID:AN000059
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:10
Offset Frequency:3293 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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