Summary of study ST000320

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 PR000259. The data can be accessed directly via it's Project DOI: 10.21228/M89K5F This work is supported by NIH grant, U2C- DK119886.

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Study IDST000320
Study TitleSingle treatment gene impact on Arabidopsis metabolites
Study SummaryThis experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2014-12-22
Num Groups6
Total Subjects34
Raw Data AvailableYes
Raw Data File Type(s).bin,.xsd,.cd,.cg,.xml
Analysis Type DetailLC-MS
Release Date2016-01-27
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M89K5F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000259
Project DOI:doi: 10.21228/M89K5F
Project Title:Single treatment gene impact on Arabidopsis metabolites
Project Summary:This experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:U24DK097154

Subject:

Subject ID:SU000340
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702
Species Group:Plant

Factors:

Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA014497Seed-111-1B111
SA014498Seed-111-2B111
SA014499Seed-111-3B111
SA014500Seed-111-1A111
SA014501Seed-111-3A111
SA014502Seed-111-2A111
SA014503Seed-133-2A133
SA014504Seed-133-2B133
SA014505Seed-133-3A133
SA014506Seed-133-1B133
SA014507Seed-133-1A133
SA014508Seed-Control-AControl
SA014509Seed-Control-BControl
SA014510Seed-Control-EControl
SA014511Seed-Control-DControl
SA014512Seed-Control-CControl
SA014513Seed-Control-FControl
Showing results 1 to 17 of 17

Collection:

Collection ID:CO000334
Collection Summary:Plants are 30-35d old. They were harvested in liquid N2, grounded to fine powder, distributed to individual falcon tubes and kept at dry ice before handing over the sample to core facility.
Collection Protocol Filename:StudyDesign-AvinashSrivastava-82514.pdf
Sample Type:Seeds

Treatment:

Treatment ID:TR000354
Treatment Summary:Single treatment gene impact on plant metabolites and compared to WT control: 1. Control (A,B,C,D,E,F total 6 replicates) 2. Sample 1 (A,B,C,D,E,F total 6 replicates) 3. Sample 2. (A,B,C,D,E,F total 6 replicates)
Treatment Protocol Filename:StudyDesign-AvinashSrivastava-82514.pdf

Sample Preparation:

Sampleprep ID:SP000348
Sampleprep Summary:-
Sampleprep Protocol Filename:Sample_Prep_Avinash_Srivastava_mx_188894.pdf

Combined analysis:

Analysis ID AN000508 AN000509
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Unspecified Unspecified
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak height Peak height

Chromatography:

Chromatography ID:CH000358
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Unspecified
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:1.67 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000444
Analysis ID:AN000508
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000445
Analysis ID:AN000509
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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