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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000032 |
| Study Title | Metabolomics Involved in Early Life Antibiotic Exposures(NOD-Cecal) |
| 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_Cecal 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: | 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 |
|---|---|---|
| SA001664 | CNC111 | Control |
| SA001665 | CNC141 | Control |
| SA001666 | CNC140 | Control |
| SA001667 | CNP126 | PAT |
| SA001668 | CNP127 | PAT |
| SA001669 | CNP124 | PAT |
| SA001670 | CPL202 | Pool QC |
| SA001671 | CPL203 | Pool QC |
| SA001672 | CPL201 | Pool QC |
| SA001673 | CPL103 | Pool QC |
| SA001674 | CPL101 | Pool QC |
| SA001675 | CPL102 | Pool QC |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000032 |
| Collection Summary: | - |
| 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 |
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 |
