Summary of Study ST000035

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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 IDST000035
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(EstroSTAT-Liver )
Study TypeMetabolomics
Study SummaryIn the EstroSTAT sub-study, a total of 18 samples from 23 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 serum 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 Low phyto-estrogen diet.
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
Submit Date2014-03-14
Num Groups2
Total Subjects6
Study CommentsEstroSTAT_Liver
Raw Data AvailableYes
Uploaded File Size400K approx
Analysis Type DetailNMR
Release Date2015-03-14
Release Version1
Susan Sumner Susan Sumner application/zip

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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
Publications:Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nature Reviews. Genetics 2012; 13; 260-270


Subject ID:SU000052
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Animal Housing:Conventional
Animal Feed:Low phyto-estrogen diet
Species Group:Mammal


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

mb_sample_id local_sample_id Treatment Group
SA001703LPL102Pooled QC
SA001704LPL103Pooled QC
SA001705LPL101Pooled QC
SA001706LPL202Pooled QC
SA001707LPL203Pooled QC
SA001708LPL201Pooled QC
Showing results 1 to 12 of 12


Collection ID:CO000035
Collection Summary:-
Sample Type:liver
Collection Time:23 weeks


Treatment ID:TR000053
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:SP000048
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:EstroSTAT_Liver_Metabolomics_Procedure.docx


Analysis ID:AN000055
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:CH000036
Num Factors:3


NMR ID:NM000017
Analysis ID:AN000055
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
Baseline Correction Method:polynomial
Chemical Shift Ref Std:DSS