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.
| Study ID | ST001634 |
| Study Title | A combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean. |
| Study Summary | This 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 Name | Renaud |
| First Name | Justin |
| Address | 1391 Sandford Street, London, Ontario, N5V 4T3, Canada |
| justin.renaud@canada.ca | |
| Phone | 519-953-6698 |
| Submit Date | 2020-12-17 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-01-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
| Species Group: | Plants |
Factors:
Subject type: Plant; Subject species: Glycine max (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA138211 | Sa_008 | GmMYB176-GmbZIP5-overexpressed |
| SA138212 | Sa_009 | GmMYB176-GmbZIP5-overexpressed |
| SA138213 | Sa_010 | GmMYB176-GmbZIP5-overexpressed |
| SA138214 | Sa_007 | GmMYB176-GmbZIP5-overexpressed |
| SA138215 | Sa_006 | GmMYB176-GmbZIP5-overexpressed |
| SA138216 | Sa_002 | Wild-type |
| SA138217 | Sa_003 | Wild-type |
| SA138218 | Sa_004 | Wild-type |
| SA138219 | Sa_005 | Wild-type |
| SA138220 | Sa_001 | Wild-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 (50 x 2.1mm,1.8um) | Agilent Zorbax RRHD EclipsePlus (50 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 | 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 (50 x 2.1mm,1.8um) |
| 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: | 100% water; 0.1% formic acid |
| Solvent B: | 100% 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 |
