Summary of Study ST000481
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 PR000353. The data can be accessed directly via it's Project DOI: 10.21228/M8DW3Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST000481 |
| Study Title | Metabolomics of Mice Cohousing and Microbiota Transfer (part II) |
| Study Summary | The mice serum samples were extracted and analyzed using broad spectrum GCMS for the identification of compounds distinguishing the groups. |
| Institute | University of North Carolina |
| Department | Discovery-Sciences-Technology (DST) |
| 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 | 2016-08-25 |
| Num Groups | 4 |
| Total Subjects | 12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2018-04-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000353 |
| Project DOI: | doi: 10.21228/M8DW3Q |
| Project Title: | Metabolomics of Mice Cohousing and Microbiota Transfer |
| Project Summary: | Metabolomics analysis was performed on twelve mice serum samples from Dr. Martin Blaser's laboratory at NYU school of medicine. Serum from week 15 mice were analyzed: (a) mice received low-dose antibiotics until week 4 (STAT), (b) mice received no antibiotics (control), (c) mice received low dose antibiotics (STAT) and then cohoused with control animals (STAT-coho), (d) mice received no antibiotics and then were cohoused with STAT animals (Control-coho). In this collaboration, we are interested in the metabolic differences among these groups. |
| Institute: | New York University |
| Department: | Langone Medical Center |
| Last Name: | Blaser |
| First Name: | Martin |
| Address: | 550 First Avenue, BCD 689, New York, NY 10016 |
| Email: | martin.blaser@nyumc.edu |
| Phone: | 646-501-4386 |
Subject:
| Subject ID: | SU000924 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA051634 | C38 | Control |
| SA051635 | C94 | Control |
| SA051636 | C97 | Control |
| SA051637 | C36 | Control-COHO |
| SA051638 | C35 | Control-COHO |
| SA051639 | C42 | Control-COHO |
| SA051640 | ExTP3 | External Study Pool |
| SA051641 | ExTP1 | External Study Pool |
| SA051642 | ExTP2 | External Study Pool |
| SA051646 | S104 | Stat |
| SA051647 | S111 | Stat |
| SA051648 | S54 | Stat |
| SA051643 | S60 | STAT-COHO |
| SA051644 | S58 | STAT-COHO |
| SA051645 | S56 | STAT-COHO |
| SA051649 | TP01 | Study Total Pool |
| SA051650 | TP02 | Study Total Pool |
| Showing results 1 to 17 of 17 |
Collection:
| Collection ID: | CO000918 |
| Collection Summary: | Serum was collected via standard operating procedures. |
| Sample Type: | blood |
| Storage Conditions: | -80 °C |
| Blood Serum Or Plasma: | Serum |
Treatment:
| Treatment ID: | TR000938 |
| Treatment Summary: | STAT | Control | STAT-COHO | Control-COHO |
| Treatment Protocol Comments: | STAT treated mice were cohoused with Control mice | Control mice were cohoused with STAT treated mice |
| Treatment Compound: | low dose antibiotics until week 4 | no antibiotics |
Sample Preparation:
| Sampleprep ID: | SP000931 |
| Sampleprep Summary: | Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers |
| Processing Method: | 30 µL of serum were added to Eppendorf tube. Add 1000 µL of 3:3:2 ACN:ISP:H20 extraction solution to aliquots, shake and centrifuge for 2 minutes at 4C and 14000 rcf to precipitate proteins. Sample was split into (2)-450 µL fractions, one fraction was archived in -80°C the second fraction was subject t complete sample processing. Transfer supernatant to a new vial. Evaporate supernatant to complete dryness at room temp. |
| Processing Storage Conditions: | On Ice and or 4⁰C cold room |
| Extraction Method: | (step 1) 3:3:2 Acetonitrile:Isopropanol:H2O, (step 2) 1:1 Acetonitrile:H2O |
| Extract Storage: | -80⁰C |
| Sample Resuspension: | Samples resuspended in 200 µL of 1:1 ACN:H2O. Evaporated to dryness w/speed vac. |
| Sample Derivatization: | Formation of methoximes by adding 10µL of 40mg/mL MeOx in pyridine to each sample. Placed onto Thermomixer for 90 min at 30⁰C. Then FAME retention index markers and MSTFA added to each sample for derivatization step. Samples returned to Thermomixer for 45 min at 70⁰C. |
| Sample Spiking: | Fatty acid methyl esters (FAME) |
Combined analysis:
| Analysis ID | AN001449 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus 4D GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC x GC-TOF |
| MS instrument name | Leco Pegasus 4D GCxGC TOF |
| Ion Mode | POSITIVE |
| Units | intensity |
Chromatography:
| Chromatography ID: | CH001018 |
| Chromatography Summary: | GCMS analysis is based on the Oliver Fiehn method |
| Instrument Name: | Leco Pegasus 4D GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Pressure: | 14.05psi |
| Column Temperature: | Initial Oven Temp 100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min. |
| Flow Gradient: | constant flow |
| Flow Rate: | 1 mL/min |
| Injection Temperature: | 250⁰C |
| Retention Index: | FAME retention index markers C8-C30 |
| Sample Injection: | 1.0 µL |
| Analytical Time: | 20 min |
| Oven Temperature: | Initial Oven Temp100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min. |
| Transferline Temperature: | 280⁰C |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001339 |
| Analysis ID: | AN001449 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Helium Flow: | 1 mL/min |
| Ion Source Temperature: | 250⁰C |
| Ionization Energy: | 70eV |
| Source Temperature: | 250⁰C |
| Resolution Setting: | 1200 |
| Scan Range Moverz: | 50-750 |
| Scanning: | 20 spectra/sec |
