Summary of Study ST000457
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
Study ID | ST000457 |
Study Title | Metabolomics of Mice Cohousing and Microbiota Transfer |
Study Summary | The mice serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer. |
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 | 2016-09-01 |
Num Groups | 4 |
Total Subjects | 12 |
Raw Data Available | Yes |
Raw Data File Type(s) | wiff |
Analysis Type Detail | LC-MS |
Release Date | 2017-10-03 |
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: | SU000478 |
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 |
---|---|---|
SA023180 | p180 QC2 | - |
SA023181 | PBS_02 | - |
SA023182 | p180 Cal6 | - |
SA023183 | PBS_01 | - |
SA023184 | p180 QC1 | - |
SA023185 | p180 QC3 | - |
SA023186 | p180 Cal1 | - |
SA023187 | p180 Cal4 | - |
SA023188 | p180 Cal5 | - |
SA023189 | p180 Cal3 | - |
SA023190 | p180 Cal2 | - |
SA023191 | p180 Cal7 | - |
SA023192 | PBS_03 | - |
SA023193 | C94 | Control |
SA023194 | C38 | Control |
SA023195 | C97 | Control |
SA023196 | C42 | Control-COHO |
SA023197 | C36 | Control-COHO |
SA023198 | C35 | Control-COHO |
SA023202 | S54 | Stat |
SA023203 | S104 | Stat |
SA023204 | S111 | Stat |
SA023199 | S60 | STAT-COHO |
SA023200 | S56 | STAT-COHO |
SA023201 | S58 | STAT-COHO |
SA023205 | TP01 | Study Total Pool |
SA023206 | TP02 | Study Total Pool |
SA023207 | TP03 | Study Total Pool |
Showing results 1 to 28 of 28 |
Collection:
Collection ID: | CO000472 |
Collection Summary: | Serum was collected via standard operating procedures. |
Sample Type: | Blood |
Treatment:
Treatment ID: | TR000492 |
Treatment Summary: | STAT - low dose antibiotics until week 4 STAT-COHO -STAT treated mice were cohoused with Control mice Control-COHO - Control mice were cohoused with STAT treated mice Control – No antibiotics |
Sample Preparation:
Sampleprep ID: | SP000485 |
Sampleprep Summary: | Sample Preparation Prior to Biocrates p180 Kit Plate Analysis: Thawed serum samples were vortexed for 30 seconds. Whole study pooled QC samples were created by combining 10 µL aliquot from each of the study samples into a 2 mL LoBind eppendorf tube. This QC pooled sample was then vortexed for 30 sec. Then, three whole study pooled QC samples of 30 µL each were aliquoted into 2 mL LoBind eppendorf tubes. Study samples were generated by aliquoting 30 µL from each original sample vial into 2 mL LoBind eppendorf tubes. For extraction, 1,000 µL of cold 3:3:2 Acetonitrile:Isopropyl Alcohol:Water (v/v/v) was added to each tube and vortexed for 5 min at 4 °C. The samples were then centrifuged at 4 °C and at 14,000 rcf for 2 min. A 450 µL aliquot of the supernatant from each sample was transferred into pre-labeled 2.0 mL LoBind eppendorf tubes and stored at -80 °C. Samples were then dried on a lyophilizer overnigh. The residue was reconstituted in 30 µL of 85:15 Ethanol:Water, v/v, and vortexed. Then, the samples were centrifuged at 4 °C for 4 min at 16,000 rcf. Biocrates Plate Preparation: A Biocrates p180 kit was prepared following the AbsoluteIDQ™ p180 Kit metabolomics procedure. Briefly, an internal standard mix was added to 95 of the 96 wells. Next, zero samples, QC standards and calibration standards were added to their corresponding wells. The study samples and pooled QC Samples (20 µL) were then added to the appropriate wells and dried for 30 minutes under nitrogen flow. The plate was derivatized using a 5% phenylisothiocyanate (PITC) solution in (1:1:1) ethanol:pyridine:water (v/v/v) and, then, incubated for 20 minutes followed by a drying step under nitrogen flow. An extraction solvent (5 mM ammonium acetate in methanol) was added to all wells. The plate was then shaken and centrifuged. After centrifugation, 150 µL was removed and transferred to a second 96-well plate (LCMS plate). This second plate was diluted with 150 µL of HPLC grade water for a subsequent LCMS (MRM analysis) for measuring amino acids and biogenic amines. All wells in the original plate were diluted with 400 µL of flow injection analysis (FIA) Running Solvent for a FIA-MS (MRM analysis) for measuring lipids, acylcarnitines, and hexose. |
Combined analysis:
Analysis ID | AN000716 | AN000717 | AN000718 |
---|---|---|---|
Analysis type | MS | MS | MS |
Chromatography type | Reversed phase | Reversed phase | Reversed phase |
Chromatography system | Agilent 1100 | Agilent 1100 | Agilent 1100 |
Column | Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) | Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) | Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) |
MS Type | ESI | ESI | ESI |
MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
Ion Mode | POSITIVE | POSITIVE | NEGATIVE |
Units | Intensity | Intensity | Intensity |
Chromatography:
Chromatography ID: | CH000515 |
Instrument Name: | Agilent 1100 |
Column Name: | Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS000636 |
Analysis ID: | AN000716 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000637 |
Analysis ID: | AN000717 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000638 |
Analysis ID: | AN000718 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | NEGATIVE |