Summary of Study ST000036
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 | ST000036 |
Study Title | Metabolomics Involved in Early Life Antibiotic Exposures(EstroSTAT-Serum) |
Study Type | Metabolomics |
Study Summary | In 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. |
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 | EstroSTAT_Serum |
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: | SU000053 |
Subject Type: | Animal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6 |
Gender: | Female |
Animal Housing: | Conventional |
Animal Feed: | Low phyto-estrogen diet |
Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Treatment Group |
---|---|---|
SA001712 | SEC906 | Control |
SA001713 | SEC922 | Control |
SA001714 | SEC920 | Control |
SA001715 | SPL102 | Pooled QC |
SA001716 | SPL103 | Pooled QC |
SA001717 | SPL101 | Pooled QC |
SA001718 | SES910 | STAT |
SA001719 | SES365 | STAT |
SA001720 | SES911 | STAT |
Showing results 1 to 9 of 9 |
Collection:
Collection ID: | CO000036 |
Collection Summary: | - |
Sample Type: | blood |
Collection Time: | 23 weeks |
Blood Serum Or Plasma: | serum |
Treatment:
Treatment ID: | TR000054 |
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: | SP000049 |
Sampleprep Summary: | Frozen serum study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 50/100 µL (sub-study dependent) were transferred into BSI-labeled eppendorf tubes. Purchased mouse sera (Sigma #S7273) was also transferred into three BSI-labeled eppendorf tubes (50/100 µL) for QC samples during analysis. Freshly prepared 0.9% Saline (wt/v) solution in 10% D2O, was added to each tube (150/100 µL) and they were vortexed for 30 seconds. Freshly prepared 10 mM Formate solution containing 2% (wt/v) NaN3 was added to each tube (50 µL) to serve as internal standard and they were vortexed for 30 seconds again, then centrifuged at 12000 rcf for 5 minutes at 4 °C. A 200 µL aliquot of the supernatant was transferred into 3 mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition. |
Sampleprep Protocol Filename: | EstroSTAT_Serum_Metabolomics_Procedure.docx |
Analysis:
Analysis ID: | AN000056 |
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: | CH000037 |
Num Factors: | 3 |
NMR:
NMR ID: | NM000018 |
Analysis ID: | AN000056 |
Instrument Name: | Bruker Avance III |
Instrument Type: | FT-NMR |
NMR Experiment Type: | 1D 1H |
Field Frequency Lock: | Deuterium |
Standard Concentration: | 1.0 mM |
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: | cpmgpr1d |
Water Suppression: | presat |
Pulse Width: | 14.84 us |
Power Level: | 25.704w |
Receiver Gain: | 4.5 |
Offset Frequency: | 3300.70 Hz |
Chemical Shift Ref Cpd: | Formate |
Temperature: | 298.1 K |
Number Of Scans: | 512 |
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: | Formate |