Summary of Study ST000026

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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Download binned data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST000026
Study TitleMetabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Cecal)
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_Cecal
Raw Data AvailableYes
Raw Data File Type(s)fid
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:SU000043
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
SA001598CDC029Control
SA001599CDC032Control
SA001600CDC030Control
SA001601CPL102Pool QC
SA001602CPL103Pool QC
SA001603CPL101Pool QC
SA001604CPL202Pool QC
SA001605CPL203Pool QC
SA001606CPL201Pool QC
SA001607CDS054STAT
SA001608CDS039STAT
SA001609CDS052STAT
Showing results 1 to 12 of 12

Collection:

Collection ID:CO000026
Sample Type:cecal contents
Collection Time:8 weeks

Treatment:

Treatment ID:TR000044
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:SP000039
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:DuraSTAT_Cecal_Metabolomics_Procedure.docx

Chromatography:

Chromatography ID:CH000027

Analysis:

Analysis ID:AN000046
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:CH000027
Num Factors:3

NMR:

NMR ID:NM000008
Analysis ID:AN000046
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:9
Offset Frequency:3296 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
  logo