Summary of Study ST000040
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 PR000018. The data can be accessed directly via it's Project DOI: 10.21228/M8Z59Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000040 |
| Study Title | Heatshock response of C. elegans using IROA (I) |
| Institute | University of Florida |
| Department | Biochemistry & Molecular Biology |
| Laboratory | Edison |
| Last Name | Stupp |
| First Name | Gregory |
| stuppie@ufl.edu | |
| Submit Date | 2013-12-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Uploaded File Size | 3.2 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2014-03-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000018 |
| Project DOI: | doi: 10.21228/M8Z59Q |
| Project Title: | Isotopic Ratio Outlier Analysis Global Metabolomics ofCaenorhabditis elegans |
| Project Type: | IROA labeling study |
| Project Summary: | We demonstrate the global metabolic analysis ofCaenorhabditis elegansstress responses using a mass-spectrometry-based technique called isotopic ratio outlier analysis (IROA). In an IROA protocol, control and experimental samples are isotopically labeled with 95 and 5%13C, and the two sample populations are mixed together for uniform extraction, sample preparation, and LC-MS analysis.To illustrate the utility of IROA for global metabolomics, we exposed wild-type (N2) worms to a heat shock (30 min heat shock at 33 C), which causes significant, widespread changes in metabolism. We collected and analyzed material from the exometabolome (all material that worms release in the supernatant) and the endometabolome (homogenized total extracts from the worm bodies). |
| Institute: | University of Florida |
| Department: | Biochemistry & Molecular Biology |
| Laboratory: | Edison |
| Last Name: | Edison |
| First Name: | Arthur |
| Address: | R3-226 Academic Research Building, Department of Biochemistry & Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245 |
| Email: | aedison@ufl.edu |
| Phone: | (352) 392-4535 |
Subject:
| Subject ID: | SU000057 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
| Genotype Strain: | N2 |
| Age Or Age Range: | Young Adult |
| Gender: | Hermaphrodite |
| Species Group: | Invertebrates |
Factors:
Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Heat shock | Metabolome |
|---|---|---|---|
| SA001760 | Control_3P | control | endometabolome |
| SA001761 | Control_1P | control | endometabolome |
| SA001762 | Control_4P | control | endometabolome |
| SA001763 | Control_2P | control | endometabolome |
| SA001764 | Control_4S | control | exometabolome |
| SA001765 | Control_3S | control | exometabolome |
| SA001766 | Control_2S | control | exometabolome |
| SA001767 | Control_1S | control | exometabolome |
| SA001768 | Test_1P | heat shock | endometabolome |
| SA001769 | Test_3P | heat shock | endometabolome |
| SA001770 | Test_2P | heat shock | endometabolome |
| SA001771 | Test_4P | heat shock | endometabolome |
| SA001772 | Test_4S | heat shock | exometabolome |
| SA001773 | Test_2S | heat shock | exometabolome |
| SA001774 | Test_1S | heat shock | exometabolome |
| SA001775 | Test_3S | heat shock | exometabolome |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO000040 |
| Collection Summary: | - |
| Sample Type: | whole young adult C. elegans Heat shock | supernatant Heat shock | whole young adult C. elegans Control | supernatant Control |
| Collection Method: | centrifugation | Filtration (0.2 micron) | centrifugation | Filtration (0.2 micron) |
| Volumeoramount Collected: | 225,000 worms | 10 mL worm water | 250,000 worms | 10 mL worm water |
Treatment:
| Treatment ID: | TR000058 |
| Treatment Summary: | Heat Shock: Two successive synchronous generations of wild-type C. elegans (N2) were grown in S-complete buffer at 22C containing 5% 13C-labeled E. coli. Upon reaching the young adult stage, the population was washed from E. coli using standard procedures and was divided into four replicates. Each replicate was treated with a 30 min heat shock at 33 °C followed by incubation at 22C for 1.5 hours. Control: Two successive synchronous generations of wild-type C. elegans (N2) were grown in S-complete buffer at 22C containing 95% 13C-labeled E. coli. Upon reaching the young adult stage, the population was washed from E. coli using standard procedures. |
| Treatment: | Abiotic |
| Treatment Dose: | 30C | 22C |
| Treatment Doseduration: | 30C for 30 minutes; 1.5 hours at 22 C before harvest | 22C for 30 minutes; 1.5 hours at 22 C before harvest |
| Animal Acclimation Duration: | - |
Sample Preparation:
| Sampleprep ID: | SP000053 |
| Sampleprep Summary: | Supernatant (endometabolome) was separated from worm pellets (exometabolome) by centrifugation. The supernatant was filtered, lyophilized, and resuspended in 100 μL of LC-MS grade H2O. Worm pellet (endometabolome)was separated from supernatant (exometabolome) by centrifugation. The worm pellets were homogenized using a Biospec Mini-Beadbeater-8 in 80% methanol, dried under nitrogen and resuspended in 100 μL of LC-MS grade H2O. |
| Processing Method: | filtration with 0.2 micron nitrocellulose, frozen at -80C, lyophilized and resuspended in 100 μL of LC-MS grade H2O. homogenization with Biospec Mini-Beadbeater-8 in 80% methanol, dried under nitrogen and resuspended in 100 μL of LC-MS grade H2O. |
Chromatography:
| Chromatography ID: | CH000041 |
| Chromatography Summary: | Three microliters of each sample were injected onto a Thermo Scientific Gold aQ (150 × 2.1 mm, 1.9 μm) column using a column temperature of 40 °C and a flow rate of 600 μL/min with a gradient of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) from 100% solvent A for 1 min followed by a linear gradient to 20% B in 6 min, a linear gradient to 60% B in 2 min, a linear gradient to 95% B in 4 min, held for 2 min, and a 3.5 min return to the starting composition. The inlet to the Orbitrap was held at a temperature of 320 °C, and the S-lens RF Level was set to 35%. The FR resolution was set to 70 000 at m/z 200. The accuracy achieved was routinely less than 1.5 ppm, externally calibrated. |
| Instrument Name: | Thermo Accela 1250 |
| Column Name: | Thermo Scientific Gold aQ |
| Column Temperature: | 40 °C |
| Flow Gradient: | A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) from 100% solvent A for 1 min followed by a linear gradient to 20% B in 6 min, a linear gradient to 60% B in 2 min, a linear gradient to 95% B in 4 min, held for 2 min, and a 3.5 min return to the starting composition |
| Sample Injection: | 3 ?L |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 18.5 min |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN000060 |
| Analysis Type: | MS |
| Instrument Name: | Thermo Scientific Q-Exactive |
| Detector Type: | Thermo Scientific Q-Exactive Orbitrap/positive mode |
| Chromatography ID: | CH000041 |
| Num Factors: | 4 |
| Num Metabolites: | 280 |
| Rt Units: | Minutes |
| Units: | Peak area |
| Analysis ID: | AN000061 |
| Analysis Type: | MS |
| Instrument Name: | Thermo Scientific Q-Exactive |
| Detector Type: | Thermo Scientific Q-Exactive Orbitrap/negative mode |
| Chromatography ID: | CH000041 |
| Num Factors: | 4 |
| Num Metabolites: | 247 |
| Rt Units: | Minutes |
| Units: | Peak area |
