Summary of study ST001634

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 PR001045. The data can be accessed directly via it's Project DOI: 10.21228/M8MQ3V This work is supported by NIH grant, U2C- DK119886.

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

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001634
Study TitleA combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean.
Study SummaryThis study identified how the GmMYB176 protein complex affects the metabolome of soybean hairy roots using non-targeted high resolution mass spectrometry.
Institute
Agriculture and Agri-Food Canada
Last NameRenaud
First NameJustin
Address1391 Sandford Street, London, Ontario, N5V 4T3, Canada
Emailjustin.renaud@canada.ca
Phone519-953-6698
Submit Date2020-12-17
Num Groups2
Total Subjects10
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-01-07
Release Version1
Justin Renaud Justin Renaud
https://dx.doi.org/10.21228/M8MQ3V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001045
Project DOI:doi: 10.21228/M8MQ3V
Project Title:A combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean
Project Type:Non-targeted high resolution MS of soybean GmMYB176-bZIP overexpressed hairy roots.
Project Summary:GmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the isoflavonoid biosynthetic pathway thereby affecting their levels in soybean roots. While GmMYB176 is important for isoflavonoid synthesis, it is not sufficient for the function and requires additional cofactor(s). The aim of this study was to identify how the GmMYB176 protein complex affects the metabolome of soybean hairy roots using non-targeted high resolution mass spectrometry.
Institute:Agriculture and Agri-Food Canada
Last Name:Renaud
First Name:Justin
Address:1391 Sandford Street, London, Ontario, N5V 4T3, Canada
Email:justin.renaud@canada.ca
Phone:519-953-6698

Subject:

Subject ID:SU001711
Subject Type:Plant
Subject Species:Glycine max
Taxonomy ID:3847
Age Or Age Range:6 days

Factors:

Subject type: Plant; Subject species: Glycine max (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA138211Sa_008GmMYB176-GmbZIP5-overexpressed
SA138212Sa_009GmMYB176-GmbZIP5-overexpressed
SA138213Sa_010GmMYB176-GmbZIP5-overexpressed
SA138214Sa_007GmMYB176-GmbZIP5-overexpressed
SA138215Sa_006GmMYB176-GmbZIP5-overexpressed
SA138216Sa_002Wild-type
SA138217Sa_003Wild-type
SA138218Sa_004Wild-type
SA138219Sa_005Wild-type
SA138220Sa_001Wild-type
Showing results 1 to 10 of 10

Collection:

Collection ID:CO001704
Collection Summary:Soybean harasoy63 seeds were planted and grown for 6 days. Cotyledons were collected after 6 days for soybean hairy root transformation. After 21 days, transgenic soybean hairy roots were collected for metabolomics
Sample Type:Plant

Treatment:

Treatment ID:TR001724
Treatment Summary:No treatment, only effects of genotype compared to wild-type was investigated

Sample Preparation:

Sampleprep ID:SP001717
Sampleprep Summary:For metabolomics analysis, frozen hairy roots were ground with liquid nitrogen and extracted in methanol:water (80:20, v/v). The samples were sonicated on ice water bath for 15 min followed by centrifugation at 11,000×g for 10 min at ambient temperature. The supernatant (350 µL) was dried under nitrogen gas. The dried pellet was dissolved in 200 µL of 50% methanol containing 10 µg caffeine as an internal standard and filtered through a 0.45 µm syringe filter.
Sampleprep Protocol ID:jrenaud_SP_Sample_preparation.pdf

Combined analysis:

Analysis ID AN002670 AN002671
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Agilent 1290
Column Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm) Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm)
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:CH001965
Chromatography Summary:An Agilent 1290 HPLC using a Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm) was used to resolve the analytes.
Instrument Name:Agilent 1290
Column Name:Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm)
Column Temperature:35
Flow Gradient:0 min, 0% B; 0.5 min, 0% B; 3.5 min, 100% B; 6 min, 100% B; 6.5 min, 0% B
Flow Rate:0.300 uL/min
Sample Injection:5 uL
Solvent A:Water + 0.1% Formic acid
Solvent B:Acetonitrile + 0.1% Formic acid
Capillary Voltage:ESI+, 3.9kV; ESI-, 3.5 kV
Chromatography Type:Reversed phase

MS:

MS ID:MS002469
Analysis ID:AN002670
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Thermo.raw files were converted to .mzml format using Protewizard , with peak peaking filter applied. Features were detected using the XCMS package with the centWave method (ppm tolerance 3.0). The signal to noise threshold was set to 5, noise was set to 5×105 and pre-filter was set to five scans with a minimum 5,000 intensity. Retention time correction was conducted using the obiwarp method.. Grouping of features was set to those present in at least 0.1% of all samples (retention time deviation 5 s; m/z width, 0.015). The ‘fillPeaks’ function was used with default settings. Zero values were imputed by 2/3 the minimum peak area value of a specific feature across all samples. PCA plots were obtained by log transforming the imputed XCMS peak area values, and ‘pareto’ scaling in Rstudio. Volcano plots were also generated using the imputed XCMS peak area values. Compounds were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and also comparison of fragmentation patterns to MS/MS databases.
Ion Mode:POSITIVE
  
MS ID:MS002470
Analysis ID:AN002671
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Thermo.raw files were converted to .mzml format using Protewizard , with peak peaking filter applied. Features were detected using the XCMS package with the centWave method (ppm tolerance 3.0). The signal to noise threshold was set to 5, noise was set to 5×105 and pre-filter was set to five scans with a minimum 5,000 intensity. Retention time correction was conducted using the obiwarp method.. Grouping of features was set to those present in at least 0.1% of all samples (retention time deviation 5 s; m/z width, 0.015). The ‘fillPeaks’ function was used with default settings. Zero values were imputed by 2/3 the minimum peak area value of a specific feature across all samples. PCA plots were obtained by log transforming the imputed XCMS peak area values, and ‘pareto’ scaling in Rstudio. Volcano plots were also generated using the imputed XCMS peak area values. Compounds were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and also comparison of fragmentation patterns to MS/MS databases.
Ion Mode:NEGATIVE
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