Summary of Study ST000034
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 | ST000034 |
| Study Title | Metabolomics Involved in Early Life Antibiotic Exposures(NOD-Serum) |
| Study Type | Metabolomics |
| Study Summary | In 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 |
| 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 | NOD_Serum Study |
| 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: | SU000051 |
| 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: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment Group |
|---|---|---|
| SA001688 | SNC111 | Control |
| SA001689 | SNC141 | Control |
| SA001690 | SNC140 | Control |
| SA001691 | SNP126 | PAT |
| SA001692 | SNP127 | PAT |
| SA001693 | SNP124 | PAT |
| SA001694 | SPL202 | Pool QC |
| SA001695 | SPL203 | Pool QC |
| SA001696 | SPL201 | Pool QC |
| SA001697 | SPL103 | Pool QC |
| SA001698 | SPL101 | Pool QC |
| SA001699 | SPL102 | Pool QC |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000034 |
| Collection Summary: | - |
| Sample Type: | blood |
| Collection Time: | 6 weeks |
| Blood Serum Or Plasma: | serum |
Treatment:
| Treatment ID: | TR000052 |
| 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: | SP000047 |
| 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: | NOD_Serum_Metabolomics_Procedure.docx |
Analysis:
| Analysis ID: | AN000054 |
| 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: | CH000035 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000016 |
| Analysis ID: | AN000054 |
| 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 |
