{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001634","ANALYSIS_ID":"AN002670","VERSION":"1","CREATED_ON":"December 22, 2020, 10:10 am"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"justin.renaud@canada.ca","PHONE":"519-953-6698","NUM_GROUPS":"2","TOTAL_SUBJECTS":"10"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Glycine max","TAXONOMY_ID":"3847","AGE_OR_AGE_RANGE":"6 days"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Sa_001",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_001_pos;Sa_001_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_002",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_002_pos;Sa_002_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_003",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_003_pos;Sa_003_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_004",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_004_pos;Sa_004_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_005",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_005_pos;Sa_005_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_006",
"Factors":{"Genotype":"GmMYB176-GmbZIP5-overexpressed"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_006_pos;Sa_006_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_007",
"Factors":{"Genotype":"GmMYB176-GmbZIP5-overexpressed"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_007_pos;Sa_007_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_008",
"Factors":{"Genotype":"GmMYB176-GmbZIP5-overexpressed"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_008_pos;Sa_008_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_009",
"Factors":{"Genotype":"GmMYB176-GmbZIP5-overexpressed"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_009_pos;Sa_009_neg"}
},
{
"Subject ID":"-",
"Sample ID":"Sa_010",
"Factors":{"Genotype":"GmMYB176-GmbZIP5-overexpressed"},
"Additional sample data":{"RAW_FILE_NAME":"Sa_010_pos;Sa_010_neg"}
}
],
"COLLECTION":{"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_SUMMARY":"No treatment, only effects of genotype compared to wild-type was investigated"},

"SAMPLEPREP":{"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"},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm)","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","COLUMN_TEMPERATURE":"35","SOLVENT_A":"Water + 0.1% Formic acid","SOLVENT_B":"Acetonitrile + 0.1% Formic acid","SAMPLE_INJECTION":"5 uL","CAPILLARY_VOLTAGE":"ESI+, 3.9kV; ESI-, 3.5 kV"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST001634_AN002670_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}