Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA240854

Local Sample ID:	C18-26-neg
Subject ID:	SU002495
Subject Type:	Plant
Subject Species:	Brassica napus
Taxonomy ID:	3708

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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
C18-26-neg	SA240854	FL030293	day 21	Developmental stage (DPI)
C18-26-neg	SA240854	FL030293	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.

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