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MB Sample ID: SA138216
Local Sample ID: | Sa_002 |
Subject ID: | SU001711 |
Subject Type: | Plant |
Subject Species: | Glycine max |
Taxonomy ID: | 3847 |
Age Or Age Range: | 6 days |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001711 |
Subject Type: | Plant |
Subject Species: | Glycine max |
Taxonomy ID: | 3847 |
Age Or Age Range: | 6 days |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Sa_002 | SA138216 | FL017576 | Wild-type | Genotype |
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 |