Summary of Study ST000032

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 IDST000032
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(NOD-Cecal)
Study TypeMetabolomics
Study SummaryIn the NOD sub-study, a total of 18 samples from 6 week old, male NOD/ShiLtj mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were exposed to PAT and 3 mice/matrix were non-exposed Controls. The mice were housed with SPF (Helicobacter neg/MNV neg) 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 CommentsNOD_Cecal Study
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:SU000049
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:NOD/ShiLtj
Gender:Male
Animal Animal Supplier:Jackson Laboratories
Animal Housing:SPF (Helicobacter neg / MNV neg)
Animal Feed:normal chow
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Treatment Group
SA001664CNC111Control
SA001665CNC141Control
SA001666CNC140Control
SA001667CNP126PAT
SA001668CNP127PAT
SA001669CNP124PAT
SA001670CPL202Pool QC
SA001671CPL203Pool QC
SA001672CPL201Pool QC
SA001673CPL103Pool QC
SA001674CPL101Pool QC
SA001675CPL102Pool QC
Showing results 1 to 12 of 12

Collection:

Collection ID:CO000032
Sample Type:cecal contents
Collection Time:6 weeks

Treatment:

Treatment ID:TR000050
Treatment Summary:Three mice were exposed to PAT and 3 mice were non-exposed controls. PAT= therapeutic dose-pulsed antibiotic treatment.
Treatment Compound:PAT

Sample Preparation:

Sampleprep ID:SP000045
Sampleprep Summary:Frozen cecal contents (cecal) samples were weighed into labeled homogenizer bead tubes. D20 was added to each tube (500 µL if less than 50 mg and 1000 µL if more than 100 mg of tissue). The samples were homogenized on a Spex Geno/Grinder for two 30 second pulses at 1750 rpm. Samples were centrifuged at 12000 rcf for 5 min. Cecal supernatants were transferred (450/700 µL) into 2.0 mL 0.2 µm nylon filter tubes and centrifuged at 16000 rcf until all the homogenate was filtered. The 200 µL remaining aliquot from each 1000 µL cecal sample was combined in a 10 mL tube and vortexed for 30 seconds to generate pooled samples for QC during analysis. Three “low” QC pools were generated by transferring 450 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes; and three “high” QC pools were generated by transferring 700 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes and also centrifuged at 16000 rcf until all the homogenate was filtered. The volume of homogenate needed to analyze 50 mg/sample and volume of D20 needed to bring the total volume to 630 µL was calculated. The calculated volumes of filtered supernatant and D20 were then transferred into BSI-labeled tubes. 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. Samples were vortexed for 30 seconds and centrifuged at 12000 rcf for 5 minutes. A 600 µL aliquot of the supernatant was then transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition.
Sampleprep Protocol Filename:NOD_Cecal_Metabolomics_Procedure.docx

Chromatography:

Chromatography ID:CH000033

Analysis:

Analysis ID:AN000052
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:CH000033
Num Factors:3

NMR:

NMR ID:NM000014
Analysis ID:AN000052
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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