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MB Sample ID: SA240886
Local Sample ID: | HILIC-2-neg |
Subject ID: | SU002495 |
Subject Type: | Plant |
Subject Species: | Brassica napus |
Taxonomy ID: | 3708 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002495 |
Subject Type: | Plant |
Subject Species: | Brassica napus |
Taxonomy ID: | 3708 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
HILIC-2-neg | SA240886 | FL030296 | day 7 | Developmental stage (DPI) |
HILIC-2-neg | SA240886 | FL030296 | 0.5 | Silicon treatment [g] |
Collection:
Collection ID: | CO002488 |
Collection Summary: | A total of 27 samples from the three treatments (PC, Si0.5 and Si1.0) were used for metabolomic analyses at 7-, 14- and 21 dpi. Hi-Q seedlings were grown in the soil-mix as previously described with/without Si amendment, inoculated with P. brassicae, and subsequently, washed thoroughly, flash-frozen in liquid nitrogen and stored at -80°C until analysis. Each biological replicate was comprised of 5 individual plants per treatment, and three biological replicates were generated from three independent experiments. A total of 27 samples were generated for transcriptomics and metabolomics analyses [3 treatments (PC, Si0.5 and Si1.0) x 3 time-points (7-, 14- and 21 dpi) x 3 biological replicates]. |
Collection Protocol Filename: | Collection_protocol |
Sample Type: | Plant |
Collection Location: | Alberta, Canada |
Collection Frequency: | 7, 14 21 DPI |
Volumeoramount Collected: | 0.07g per sample |
Storage Conditions: | -80℃ |
Collection Vials: | 2 mL round-bottom Eppendorf tubes |
Storage Vials: | 2 mL round-bottom Eppendorf tubes |
Collection Tube Temp: | -20 |
Treatment:
Treatment ID: | TR002507 |
Treatment Summary: | Sodium silicate (Na2SiO3, Mol. Wt: 122.06 g/L), obtained from Sigma-Aldrich (St. Louis, US), was mixed with 100 g Sunshine Professional Growing Mix (Sun Gro Horticulture, Seba Beach, Canada) and the following mixtures (treatments) were produced: 0.0 g Si (control), 0.1 g Si (Si:soil in 1:1000, wt/wt), 0.25 g (Si:soil in 1:400, wt/wt), 0.5 g (Si:soil in 1:200, wt/wt), 0.75 g (Si:soil in 3:400, wt/wt) and 1.0 g (Si:soil in 1:100, wt/wt). These treatments, hereafter, reported as Si0.0 or PC, Si0.1, Si0.25, Si0.5, Si0.75 and Si1.0, respectively. After mixing thoroughly, the pH of the soil mix was determined prior to seeding. A clubroot susceptible spring canola (Brassica napus L.) cultivar Hi-Q, developed at the University of Alberta, was used in this study. The plants were grown under greenhouse conditions (22/19°C and 16/8h photoperiod) on the above-mentioned six soil media (treatments) containing varying concentration of Si. A total of 30 plants, from three replications of each treatment (i.e. 10 plants per replication) were used. A single spore suspension of P. brassicae pathotype 3, classified as pathotype 3H (P3H) under the Canadian Clubroot Differential (CCD) set, was prepared by homogenizing the clubroot galls, and used to inoculate the seedlings following previously described procedures. |
Sample Preparation:
Sampleprep ID: | SP002501 |
Sampleprep Summary: | A total of 27 samples from the three treatments (PC, Si0.5 and Si1.0) were used for metabolomic analyses at 7-, 14- and 21 dpi. Hi-Q seedlings were grown in the soil-mix as previously described with/without Si amendment, inoculated with P. brassicae, and subsequently, washed thoroughly, flash-frozen in liquid nitrogen and stored at -80°C until analysis. Each biological replicate was comprised of 5 individual plants per treatment, and three biological replicates were generated from three independent experiments. A total of 27 samples were generated for transcriptomics and metabolomics analyses [3 treatments (PC, Si0.5 and Si1.0) x 3 time-points (7-, 14- and 21 dpi) x 3 biological replicates]. |
Sampleprep Protocol Filename: | Sample Prep protocol |
Processing Storage Conditions: | -20℃ |
Extraction Method: | 50% ACN |
Extract Cleanup: | HLB SPE |
Extract Storage: | -20℃ |
Sample Resuspension: | Primary metabolites - 90% ACN, glucosinolates - 5% ACN |
Sample Spiking: | Primary metabolites - Labeled amino acid mix; Glucosinolates - labeled CK mix |
Combined analysis:
Analysis ID | AN003920 | AN003921 | AN003922 | AN003923 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Phenomonex Kinetex C18 (50 x 2.1mm, 2.6um) | Phenomonex Kinetex C18 (50 x 2.1mm, 2.6um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | normalized relative level | normalized relative level | normalized relative level | normalized relative level |
Chromatography:
Chromatography ID: | CH002901 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) |
Column Temperature: | RT |
Flow Gradient: | Mobile phase 100% B decreased to 90% over 2.5 min and to 50% over the next 5 min and returned to 100% over 0.5 min for 12 min of column re-equilibration. |
Flow Rate: | 0.2 ml/min |
Injection Temperature: | 4 |
Solvent A: | 100% water; 10 mM ammonium bicarbonate |
Solvent B: | 95% acetonitrile; 10 mM ammonium bicarbonate |
Chromatography Type: | HILIC |
Chromatography ID: | CH002902 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Phenomonex Kinetex C18 (50 x 2.1mm, 2.6um) |
Column Temperature: | RT |
Flow Gradient: | Mobile phase 100% A held for 1.25 min, then decreased to 50% over 1.75 min and to 0% over the next 0.5 min, held at 0% for 2 min and returned to 100% over 0.5 min for 4 min of column re-equilibration. |
Flow Rate: | 0.3 ml/min |
Injection Temperature: | 4 |
Solvent A: | 100% water; 0.08% acetic acid |
Solvent B: | 100% acetonitrile; 0.08% acetic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003658 |
Analysis ID: | AN003920 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Processing of the full scan and ddMS2 data was conducted using the Xcalibur 4.1 software (Thermo Scientific, Waltham, US). Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). |
Ion Mode: | POSITIVE |
MS ID: | MS003659 |
Analysis ID: | AN003921 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Processing of the full scan and ddMS2 data was conducted using the Xcalibur 4.1 software (Thermo Scientific, Waltham, US). Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). |
Ion Mode: | NEGATIVE |
MS ID: | MS003660 |
Analysis ID: | AN003922 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Processing of the full scan and ddMS2 data was conducted using the Xcalibur 4.1 software (Thermo Scientific, Waltham, US). Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). |
Ion Mode: | POSITIVE |
MS ID: | MS003661 |
Analysis ID: | AN003923 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Processing of the full scan and ddMS2 data was conducted using the Xcalibur 4.1 software (Thermo Scientific, Waltham, US). Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). |
Ion Mode: | NEGATIVE |