Summary of Study ST000100

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 PR000092. The data can be accessed directly via it's Project DOI: 10.21228/M81S38 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000100
Study TitleGlobal Metabolomics of C. elegans using an augmented reference IROA design
Study Typeheat shock
Study SummaryGlobal Metabolomics of C. elegans using an augmented reference IROA design
Institute
University of Florida
DepartmentBiochemistry & Molecular Biology
LaboratoryArthur Edison
Last NameEdison
First NameArthur
AddressR3-226 Academic Research Building, Department of Biochemistry & Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245
Emailaedison@ufl.edu
Submit Date2014-09-13
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Uploaded File Size16 G
Analysis Type DetailLC-MS
Release Date2015-02-03
Release Version1
Arthur Edison Arthur Edison
https://dx.doi.org/10.21228/M81S38
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000092
Project DOI:doi: 10.21228/M81S38
Project Title:Global Metabolomics of C. elegans using an augmented reference IROA design
Institute:University of Florida
Department:Biochemistry & Molecular Biology
Last Name:Edison
First Name:Arthur
Address:R3-226 Academic Research Building, Department of Biochemistry & Molecular Biology, PO Box 100245, Gainesville, Fl
Email:aedison@ufl.edu
Phone:(352) 392-4535
Funding Source:NIH

Subject:

Subject ID:SU000119
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 Labelling Experimentalgroup
SA0055153PC-50.05 heat-shock
SA0055162PC-50.05 heat-shock
SA0055177PC-50.05 heat-shock
SA0055184PC-50.05 heat-shock
SA0055195PC-50.05 heat-shock
SA0055206PC-50.05 heat-shock
SA0055218PC-50.05 heat-shock
SA00552211PC-50.05 heat-shock
SA00552310PC-50.05 heat-shock
SA0055249PC-50.05 heat-shock
SA00552512PC-50.05 heat-shock
SA0055261PC-50.05 heat-shock
SA0055278PHS-50.05 no heat-shock
SA0055287PHS-50.05 no heat-shock
SA0055296PHS-50.05 no heat-shock
SA0055309PHS-50.05 no heat-shock
SA00553112PHS-50.05 no heat-shock
SA0055325PHS-50.05 no heat-shock
SA00553310PHS-50.05 no heat-shock
SA0055341PHS-50.05 no heat-shock
SA00553511PHS-50.05 no heat-shock
SA0055362PHS-50.05 no heat-shock
SA0055374PHS-50.05 no heat-shock
SA0055383PHS-50.05 no heat-shock
SA0055398PC-950.95 heat-shock
SA0055402PC-950.95 heat-shock
SA0055413PC-950.95 heat-shock
SA0055427PC-950.95 heat-shock
SA0055435PC-950.95 heat-shock
SA0055444PC-950.95 heat-shock
SA0055459PC-950.95 heat-shock
SA0055461PC-950.95 heat-shock
SA00554711PC-950.95 heat-shock
SA0055486PC-950.95 heat-shock
SA00554912PC-950.95 heat-shock
SA00555010PC-950.95 heat-shock
SA0055516PHS-950.95 no heat-shock
SA0055527PHS-950.95 no heat-shock
SA0055538PHS-950.95 no heat-shock
SA0055549PHS-950.95 no heat-shock
SA0055551PHS-950.95 no heat-shock
SA00555611PHS-950.95 no heat-shock
SA00555710PHS-950.95 no heat-shock
SA00555812PHS-950.95 no heat-shock
SA0055592PHS-950.95 no heat-shock
SA0055604PHS-950.95 no heat-shock
SA0055613PHS-950.95 no heat-shock
SA0055625PHS-950.95 no heat-shock
Showing results 1 to 48 of 48

Collection:

Collection ID:CO000102
Collection Summary:Each flask was separated into supernatant (exometabolome) and worm pellet (endometabolome) by centrifugation 2,000 rpm for 2 min.
Collection Protocol ID:Centrifugation
Collection Protocol Filename:Experimental_Methods.docx
Sample Type:Worms
Volumeoramount Collected:25,000 worms in 2.5 mL

Treatment:

Treatment ID:TR000120
Treatment Summary:Samples were treated with a 20 min heat shock at 33 °C followed by incubation at 22C for 100 min. Sample shook at 250 rpm at a worm density of 10,000 worms per mL./ Samples were incubated at 22C for 120 min. Sample shook at 250 rpm at a worm density of 10,000 worms per mL.
Treatment Protocol ID:Test/Control

Sample Preparation:

Sampleprep ID:SP000115
Sampleprep Summary:-
Sampleprep Protocol ID:Endometabolome
Sampleprep Protocol Filename:Experimental_Methods.docx
Sampleprep Protocol Comments:The worm pellets were homogenized using a FastPrep-24 (MP Biomedicals) using Lysing Matrix E tubes for 5 cycles of 60 sec in 80% methanol and then frozen at -80 °C.
Processing Method:Homogenization

Combined analysis:

Analysis ID AN000165 AN000166
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column Waters Acquity HSS T3 (100 x 2.1mm,1.8um) Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
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

Chromatography:

Chromatography ID:CH000114
Chromatography Summary:Samples were analyzed using a mass range of m/z 70-1000 in positive and negative ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass spectrometer equipped with a Dionex UltiMate 3000 RS autosampler and pump. Three ?L of each sample were injected onto an Acquity UPLC HSS T3 (2.1x100 mm, 1.8 micron) column using a column temperature of 35 C and a flow rate of 300 L/min with solvent A (0.1% formic acid in water (Fisher LC-MS Optima)) held at 100% A for 1 min, followed by linear increase to 80% B (0.1% formic acid in acetonitrile) over 10 min, kept constant for 2 min, followed by a return to initial conditions over 0.5 min and equilibration for 3 min.
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:A held at 100% A for 1 min, followed by linear increase to 80% B over 10 min, kept constant for 2 min, followed by a return to initial conditions over 0.5 min and equilibration for 3 min
Flow Rate:300 L/min
Sample Injection:3 ?L
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS000134
Analysis ID:AN000165
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The Q-Exactive was equipped with a Heated Electrospray Ionization (HESI) source which operated at a spray temperature of 350 ?C, a spray voltage of 3.5 kV, and sheath and auxiliary gas flow rates of 50 and 10 arbitrary units, respectively. The capillary temperature was held at 325 ?C, and the S-lens RF Level was set to 40%. The FR resolution was set to 70,000 at m/z 200. The accuracy achieved was routinely less than 1.5 ppm.
Ion Mode:POSITIVE
Capillary Temperature:325 ?C
Ion Source Temperature:350 ?C
Ion Spray Voltage:3.5 kV
Resolution Setting:70000
  
MS ID:MS000135
Analysis ID:AN000166
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The Q-Exactive was equipped with a Heated Electrospray Ionization (HESI) source which operated at a spray temperature of 350 ?C, a spray voltage of 3.5 kV, and sheath and auxiliary gas flow rates of 50 and 10 arbitrary units, respectively. The capillary temperature was held at 325 ?C, and the S-lens RF Level was set to 40%. The FR resolution was set to 70,000 at m/z 200. The accuracy achieved was routinely less than 1.5 ppm.
Ion Mode:NEGATIVE
Capillary Temperature:325 ?C
Ion Source Temperature:350 ?C
Ion Spray Voltage:3.5 kV
Resolution Setting:70000
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