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.

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Study IDST000481
Study TitleMetabolomics of Mice Cohousing and Microbiota Transfer (part II)
Study SummaryThe mice serum samples were extracted and analyzed using broad spectrum GCMS for the identification of compounds distinguishing the groups.
Institute
University of North Carolina
DepartmentDiscovery-Sciences-Technology (DST)
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2016-08-25
Num Groups4
Total Subjects12
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2018-04-10
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8DW3Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA051634C38Control
SA051635C94Control
SA051636C97Control
SA051637C36Control-COHO
SA051638C35Control-COHO
SA051639C42Control-COHO
SA051640ExTP3External Study Pool
SA051641ExTP1External Study Pool
SA051642ExTP2External Study Pool
SA051646S104Stat
SA051647S111Stat
SA051648S54Stat
SA051643S60STAT-COHO
SA051644S58STAT-COHO
SA051645S56STAT-COHO
SA051649TP01Study Total Pool
SA051650TP02Study 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 MS (30 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 MS (30 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
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