Summary of Study ST000242
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 PR000195. The data can be accessed directly via it's Project DOI: 10.21228/M8630S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000242 |
| Study Title | Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium |
| Study Type | differential metabolomics |
| Study Summary | Media was flash frozen with N2 and stored at -80 C. Samples can be stored at -80 C until use. ~1 ml aliquots. The following media has been provided to the metabolomics core in biological triplicates. Complete (Whole) Media: 1) Whole unconditioned medium (Defined culture media, M199) 2) Whole M1 medium 3) Whole M2 medium |
| Institute | Mayo Clinic |
| Department | Physiology and Biomedical Engineering |
| Last Name | Farrugia |
| First Name | Gianrico |
| Dasari.Surendra@mayo.edu | |
| Submit Date | 2015-06-26 |
| Num Groups | 1 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-07-08 |
| Release Version | 2 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000195 |
| Project DOI: | doi: 10.21228/M8630S |
| Project Title: | Metabolimic Analysis of Conditioned Macrophage Media |
| Project Type: | Untargeted LC-MS Metabolomics |
| Project Summary: | We are studying the secreted components from pro-inflammatory macrophages, coined M1. We use a macrophage at the opposite end of the macrophage phenotype spectrum as a control, the anti-inflammatory macrophage, coined M2. M1 macrophage conditioned media has a <3 kD factor that reduces survival of a cell of interest in primary culture. This factor is not present in M2 macrophage conditioned media <3 kD, as there is no effect on primary cell numbers. The goal of this project is to analyze the components present in the M1 conditioned <3 kD media and compare to the M2 conditioned < 3kD media. |
| Institute: | Mayo Clinic |
| Department: | Physiology and Biomedical Engineering |
| Last Name: | Farrugia |
| First Name: | Gianrico |
| Address: | 200 First Street SW, Rochester, MN 55905 |
| Email: | Dasari.Surendra@mayo.edu |
| Phone: | 507-284-0513 |
Subject:
| Subject ID: | SU000262 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Status |
|---|---|---|
| SA011163 | ms5047-2-3 | Whole M1 medium |
| SA011164 | ms5047-2-2 | Whole M1 medium |
| SA011165 | ms5047-2-1 | Whole M1 medium |
| SA011166 | ms5047-3-3 | Whole M2 medium |
| SA011167 | ms5047-3-1 | Whole M2 medium |
| SA011168 | ms5047-3-2 | Whole M2 medium |
| SA011160 | ms5047-1-3 | Whole unconditioned medium (Defined culture media, M199) |
| SA011161 | ms5047-1-2 | Whole unconditioned medium (Defined culture media, M199) |
| SA011162 | ms5047-1-1 | Whole unconditioned medium (Defined culture media, M199) |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO000253 |
| Collection Summary: | Whole media |
| Sample Type: | Media |
Treatment:
| Treatment ID: | TR000273 |
| Treatment Summary: | Media was flash frozen with N2 and stored at -80 C. Samples can be stored at -80 C until use. ~1 ml aliquots. The following media has been provided to the metabolomics core in biological triplicates. Complete (Whole) Media:1) Whole unconditioned macrophage medium (Defined culture media, M199)2) Whole M1 macrophage medium 3) Whole M2 macrophage medium |
Sample Preparation:
| Sampleprep ID: | SP000267 |
| Sampleprep Summary: | Quality-control samples used in the study were prepared from pooled samples spiked with a selection of standards. All samples (200 μL) were thawed on ice at 4°C followed by deproteinization with methanol (1:4 ratio of plasma to methanol) and vortexed for 10 s, followed by incubation at −20°C for 2 h. The samples were then centrifuged at 15,871g for 30 min at 4°C. The supernatants were lyophilized (Savant, Holbrook, NY) and stored at −20°C prior to analysis. The samples were reconstituted in 50% H2O/acetonitrile and passed through a Microcon YM3 filter (Millipore Corporation). The supernatants were transferred to analytical vials, stored in the autosampler at 4°C, and analyzed within 48 h of reconstitution in buffer. |
Chromatography:
| Chromatography ID: | CH000271 |
| Chromatography Summary: | C18 |
| Chromatography Comments: | Metabolite separation was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters high-strength silica (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN000375 |
| Analysis Type: | MS |
| Instrument Name: | Agilent 6220 TOF MS |
| Chromatography ID: | CH000271 |
| Num Factors: | 3 |
| Num Metabolites: | 85 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Units: | Peak area |
| Analysis ID: | AN000376 |
| Analysis Type: | MS |
| Instrument Name: | Agilent 6220 TOF MS |
| Chromatography ID: | CH000271 |
| Num Factors: | 3 |
| Num Metabolites: | 15 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Units: | Peak area |
| Analysis ID: | AN000377 |
| Analysis Type: | MS |
| Instrument Name: | Agilent 6220 TOF MS |
| Chromatography ID: | CH000271 |
| Num Factors: | 3 |
| Num Metabolites: | 250 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Units: | Peak area |
| Analysis ID: | AN000378 |
| Analysis Type: | MS |
| Instrument Name: | Agilent 6220 TOF MS |
| Chromatography ID: | CH000271 |
| Num Factors: | 3 |
| Num Metabolites: | 49 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Units: | Peak area |
