Summary of Study ST000028
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
| Study ID | ST000028 |
| Study Title | Metabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Urine) |
| Study Type | Metabolomics |
| Study Summary | In 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 |
| Department | Systems and Translational Sciences |
| Laboratory | Sumner Lab |
| Last Name | Sumner |
| First Name | Susan |
| Address | Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081 |
| susan_sumner @unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2014-03-14 |
| Num Groups | 2 |
| Total Subjects | 6 |
| Study Comments | DuraSTAT_Urine |
| Raw Data Available | Yes |
| Uploaded File Size | 400K approx |
| Analysis Type Detail | NMR |
| Release Date | 2015-03-14 |
| Release Version | 1 |
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: | SU000045 |
| 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 |
|---|---|---|
| SA001622 | UDC029 | Control |
| SA001623 | UDC032 | Control |
| SA001624 | UDC030 | Control |
| SA001625 | UPL102 | Pool QC |
| SA001626 | UPL103 | Pool QC |
| SA001627 | UPL101 | Pool QC |
| SA001628 | UDS052 | STAT |
| SA001629 | UDS039 | STAT |
| SA001630 | UDS054 | STAT |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO000028 |
| Collection Summary: | - |
| Sample Type: | urine |
| Collection Time: | 8 weeks |
Treatment:
| Treatment ID: | TR000046 |
| 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: | SP000041 |
| Sampleprep Summary: | Frozen urine study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 400 µL were transferred into BSI-labeled eppendorf tubes. Aliquots of 100 µL per study sample were also transferred into a 10 mL tube to generate pooled samples for QC during analysis, and 400 µL was transferred into BSI-labeled eppendorf tubes. D2O (230 µL) was added to each 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) to the tubes. Tubes were vortexed for 30 seconds and centrifuged at 12000 rcf for 5min. A 600 µL aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition. |
| Sampleprep Protocol Filename: | DuraSTAT_Urine_Metabolomics_Procedure.docx |
Analysis:
| Analysis ID: | AN000048 |
| Laboratory Name: | RTI/ DHHMRI |
| Analysis Type: | NMR |
| Analysis Comments: | NMR (700 MHz) |
| Acquisition Date: | 41522 |
| 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: | CH000029 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000010 |
| Analysis ID: | AN000048 |
| 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: | 4 |
| Offset Frequency: | 3293.10 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 |
