Summary of Study ST000030
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 | ST000030 |
| Study Title | Metabolomics Involved in Early Life Antibiotic Exposures(TranSTAT-Liver) |
| Study Type | Metabolomics |
| Study Summary | In the TranSTAT sub-study, a total of 18 samples from 8 week old, female Swiss webster mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were inoculated with cecal contents from STAT mice and 3 mice/matrix were inoculated with cecal contents from Control mice. 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 | TranSTAT_Liver 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: | SU000047 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Swiss Webster Mice |
| Gender: | Female |
| Animal Animal Supplier: | Taconic |
| 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 |
|---|---|---|
| SA001643 | LTC001 | Control |
| SA001644 | LTC005 | Control |
| SA001645 | LTC003 | Control |
| SA001646 | LPL102 | Pooled QC |
| SA001647 | LPL103 | Pooled QC |
| SA001648 | LPL101 | Pooled QC |
| SA001649 | LPL202 | Pooled QC |
| SA001650 | LPL203 | Pooled QC |
| SA001651 | LPL201 | Pooled QC |
| SA001652 | LTS008 | STAT |
| SA001653 | LTS002 | STAT |
| SA001654 | LTS005 | STAT |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000030 |
| Collection Summary: | - |
| Sample Type: | liver |
| Collection Time: | 8 weeks |
Treatment:
| Treatment ID: | TR000048 |
| Treatment Summary: | Three mice were inoculated with cecal contents from STAT mice and 3 mice were inoculated with cecal contents from control mice. STAT = sub-therapeutic antibiotic treatment. |
| Treatment Route: | cecal transfer |
Sample Preparation:
| Sampleprep ID: | SP000043 |
| Sampleprep Summary: | Frozen liver samples were weighed (50-100 mg) into labeled homogenizer bead tubes. Cold acetonitrile:water (50%) was added to tissue based on weight to make 1 mg/mL homogenates. The samples were extracted and homogenized on a Spex Geno/Grinder for two 45 second pulses at 1750 rpm. Samples were centrifuged at 12000 rcf for 5 min. Liver supernatants were transferred into BSI-labeled tubes. A 500 μL aliquot/sample was transferred into a second set of BSI-labeled tubes for further processing. To make pooled samples, a 300 μL aliquot of selected TranSTAT liver supernatants was combined in a 2 mL tube and used for QC samples in DuraSTAT, TranSTAT, EstroSTAT and NOD sub-studies. Additionally, a 200 μL aliquot of selected VG STAT liver supernatants was combined in a separate 2 mL tube and used as QC samples in the VG STAT sub-study. Three 500 μL aliquots were transferred into BSI-labeled tubes for each set of Pooled QC samples. All samples were then dried on an Eppendorf rotaVap (V-AL setting) at 30°C until dry and stored at -80 °C. On the second day of processing, 630 μL of D2O was added into each dried liver extract 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), and the samples were vortexed on a multi-tube vortexer for 10 minutes at speed 5. Tubes were then centrifuged at 12000 rcf for 5 minutes and a 600 μL aliquot of the supernatant was transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition. |
| Sampleprep Protocol Filename: | TranSTAT_Liver_Metabolomics_Procedure.docx |
Analysis:
| Analysis ID: | AN000050 |
| 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: | CH000031 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000012 |
| Analysis ID: | AN000050 |
| 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 |
