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.

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Study IDST000040
Study TitleHeatshock response of C. elegans using IROA (I)
Institute
University of Florida
DepartmentBiochemistry & Molecular Biology
LaboratoryEdison
Last NameStupp
First NameGregory
Emailstuppie@ufl.edu
Submit Date2013-12-10
Raw Data AvailableYes
Raw Data File Type(s).raw (binary files)
Uploaded File Size3.2 G
Analysis Type DetailLC-MS
Release Date2014-03-05
Release Version1
Gregory Stupp Gregory Stupp
https://dx.doi.org/10.21228/M8Z59Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Invertebrate

Factors:

Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)

mb_sample_id local_sample_id Heat shock Metabolome
SA001760Control_3Pcontrol endometabolome
SA001761Control_1Pcontrol endometabolome
SA001762Control_4Pcontrol endometabolome
SA001763Control_2Pcontrol endometabolome
SA001764Control_4Scontrol exometabolome
SA001765Control_3Scontrol exometabolome
SA001766Control_2Scontrol exometabolome
SA001767Control_1Scontrol exometabolome
SA001768Test_1Pheat shock endometabolome
SA001769Test_3Pheat shock endometabolome
SA001770Test_2Pheat shock endometabolome
SA001771Test_4Pheat shock endometabolome
SA001772Test_4Sheat shock exometabolome
SA001773Test_2Sheat shock exometabolome
SA001774Test_1Sheat shock exometabolome
SA001775Test_3Sheat shock exometabolome
Showing results 1 to 16 of 16

Collection:

Collection ID:CO000040
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.

Combined analysis:

Analysis ID AN000060 AN000061
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Accela 1250 Thermo Accela 1250
Column Thermo Scientific Gold aQ Thermo Scientific Gold aQ
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

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:0.1% formic acid in water
Solvent B:0.1% formic acid in acetonitrile
Analytical Time:18.5 min
Chromatography Type:Reversed phase

MS:

MS ID:MS000041
Analysis ID:AN000060
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Samples were analyzed using a mass range of m/z 70-800 in positive and negative ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass spectrometer equipped with an Open Accela autosampler and an Accela 1250 pump (San Jose, CA). The Q-Exactive was equipped with a heated electrospray ionization (HESI) source, which operated at a spray temperature of 500 °C, a spray voltage of 3 kV, and sheath and auxiliary gas flow rates of 60 and 10 arbitrary units, respectively. Features were extracted from the ms data using proprietary MATLAB IROA scripts. Ratios for each feature (heatshock/control) were calculated for each replicate. Ratios were normalized by setting the median log-fold change for each sample to zero
Ion Mode:POSITIVE
Ion Source Temperature:500 °C
Ion Spray Voltage:3 kV
Mass Accuracy:1.5 ppm
Scan Range Moverz:70-1000
  
MS ID:MS000042
Analysis ID:AN000061
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Samples were analyzed using a mass range of m/z 70-800 in positive and negative ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass spectrometer equipped with an Open Accela autosampler and an Accela 1250 pump (San Jose, CA). The Q-Exactive was equipped with a heated electrospray ionization (HESI) source, which operated at a spray temperature of 500 °C, a spray voltage of 3 kV, and sheath and auxiliary gas flow rates of 60 and 10 arbitrary units, respectively. Features were extracted from the ms data using proprietary MATLAB IROA scripts. Ratios for each feature (heatshock/control) were calculated for each replicate. Ratios were normalized by setting the median log-fold change for each sample to zero
Ion Mode:NEGATIVE
Ion Source Temperature:500 °C
Ion Spray Voltage:3 kV
Mass Accuracy:1.5 ppm
Scan Range Moverz:70-1000
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