Summary of Study ST002406

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 PR001548. The data can be accessed directly via it's Project DOI: 10.21228/M8M42M 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	ST002406
Study Title	Silicon ameliorates clubroot responses in canola (Brassica napus): A “multi-omics”-based investigation into possible mechanisms
Study Type	Timecourse experiment
Study Summary	Clubroot disease, caused by Plasmodiophora brassicae Woronin results in severe yield losses in Brassica crops, including canola. Silicon (Si) mitigates several stresses and enhances plant resistance to phytopathogens. We investigated the effects of Si on clubroot disease symptoms in canola at two concentrations of Si (Si1.0 and Si0.5). In addition, the effects of Si on P. brassicae-induced gene expression, endogenous levels of phytohormones and metabolites were also studied. Si application reduced clubroot symptoms and improved plant growth under greenhouse conditions. Pathogen-induced transcript-level changes were affected by Si treatment to P. brassicae with genes related to antioxidant activity, phytohormone biosynthesis and signalling, nitrogen metabolism and secondary metabolism exhibiting differential expression. Endogenous levels of several phytohormones (e.g., auxin, cytokinin, salicylic acid and abscisic acid), amino acids and secondary metabolites (e.g., glucosinolates) were affected by Si. This is the first report that Si ameliorates clubroot symptoms and its possible mode of action.
Institute	Trent University
Department	Biology
Laboratory	Emery Lab
Last Name	Kisiala
First Name	Anna
Address	1600 West Bank Drive, Trent University, Peterborough, ON, K9L 0G2, Canada
Email	annakisiala@trentu.ca
Phone	7057481011
Submit Date	2022-12-12
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2023-01-04
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001548
Project DOI:	doi: 10.21228/M8M42M
Project Title:	Silicon ameliorates clubroot responses in canola (Brassica napus): A “multi-omics”-based investigation into possible mechanisms
Project Type:	MS quantitative analysis
Project Summary:	Clubroot disease, caused by Plasmodiophora brassicae Woronin results in severe yield losses in Brassica crops, including canola. Silicon (Si) mitigates several stresses and enhances plant resistance to phytopathogens. We investigated the effects of Si on clubroot disease symptoms in canola at two concentrations of Si (Si1.0 and Si0.5). In addition, the effects of Si on P. brassicae-induced gene expression, endogenous levels of phytohormones and metabolites were also studied. Si application reduced clubroot symptoms and improved plant growth under greenhouse conditions. Pathogen-induced transcript-level changes were affected by Si treatment to P. brassicae with genes related to antioxidant activity, phytohormone biosynthesis and signalling, nitrogen metabolism and secondary metabolism exhibiting differential expression. Endogenous levels of several phytohormones (e.g., auxin, cytokinin, salicylic acid and abscisic acid), amino acids and secondary metabolites (e.g., glucosinolates) were affected by Si. This is the first report that Si ameliorates clubroot symptoms and its possible mode of action.
Institute:	Trent University
Department:	Biology
Laboratory:	Emery Lab
Last Name:	Kisiala
First Name:	Anna
Address:	1600 West Bank Drive, Trent University, Peterborough, ON, K9L 0G2, Canada
Email:	annakisiala@trentu.ca
Phone:	7057481011
Funding Source:	Alberta Agriculture and Forestry
Contributors:	Ananya Sarkar, Anna Kisiala, Dinesh Adhikary, Urmila Basu, Neil Emery, Rahman, Nat N. V. Kav

Subject:

Subject ID:	SU002495
Subject Type:	Plant
Subject Species:	Brassica napus
Taxonomy ID:	3708

Factors:

Subject type: Plant; Subject species: Brassica napus (Factor headings shown in green)

mb_sample_id	local_sample_id	Developmental stage (DPI)	Silicon treatment [g]
SA240789	HILIC-13-neg	day 14	0.0
SA240790	C18-16-pos	day 14	0.0
SA240791	C18-10-pos	day 14	0.0
SA240792	HILIC-13-pos	day 14	0.0
SA240793	C18-16-neg	day 14	0.0
SA240794	C18-13-pos	day 14	0.0
SA240795	C18-10-neg	day 14	0.0
SA240796	HILIC-10-pos	day 14	0.0
SA240797	HILIC-10-neg	day 14	0.0
SA240798	HILIC-16-neg	day 14	0.0
SA240799	C18-13-neg	day 14	0.0
SA240800	HILIC-16-pos	day 14	0.0
SA240801	C18-19-neg	day 14	0.0
SA240802	HILIC-19-neg	day 14	0.0
SA240803	C18-19-pos	day 14	0.0
SA240804	HILIC-19-pos	day 14	0.0
SA240805	C18-11-neg	day 14	0.5
SA240806	HILIC-11-pos	day 14	0.5
SA240807	C18-11-pos	day 14	0.5
SA240808	C18-20-neg	day 14	0.5
SA240809	HILIC-20-neg	day 14	0.5
SA240810	HILIC-20-pos	day 14	0.5
SA240811	HILIC-11-neg	day 14	0.5
SA240812	C18-20-pos	day 14	0.5
SA240813	C18-14-neg	day 14	0.5
SA240814	HILIC-14-neg	day 14	0.5
SA240815	C18-14-pos	day 14	0.5
SA240816	HILIC-17-pos	day 14	0.5
SA240817	C18-17-neg	day 14	0.5
SA240818	C18-17-pos	day 14	0.5
SA240819	HILIC-17-neg	day 14	0.5
SA240820	HILIC-14-pos	day 14	0.5
SA240821	HILIC-15-pos	day 14	1.0
SA240822	HILIC-15-neg	day 14	1.0
SA240823	C18-15-neg	day 14	1.0
SA240824	C18-15-pos	day 14	1.0
SA240825	HILIC-12-neg	day 14	1.0
SA240826	C18-18-pos	day 14	1.0
SA240827	C18-18-neg	day 14	1.0
SA240828	HILIC-21-pos	day 14	1.0
SA240829	HILIC-21-neg	day 14	1.0
SA240830	C18-21-neg	day 14	1.0
SA240831	C18-21-pos	day 14	1.0
SA240832	HILIC-18-neg	day 14	1.0
SA240833	HILIC-12-pos	day 14	1.0
SA240834	HILIC-18-pos	day 14	1.0
SA240835	C18-12-neg	day 14	1.0
SA240836	C18-12-pos	day 14	1.0
SA240837	HILIC-9-pos	day 14	1.0
SA240838	HILIC-9-neg	day 14	1.0
SA240839	HILIC-22-pos	day 21	0.0
SA240840	HILIC-25-pos	day 21	0.0
SA240841	C18-25-neg	day 21	0.0
SA240842	C18-22-neg	day 21	0.0
SA240843	HILIC-22-neg	day 21	0.0
SA240844	C18-25-pos	day 21	0.0
SA240845	HILIC-25-neg	day 21	0.0
SA240846	C18-22-pos	day 21	0.0
SA240847	C18-23-neg	day 21	0.5
SA240848	C18-23-pos	day 21	0.5
SA240849	HILIC-23-pos	day 21	0.5
SA240850	HILIC-23-neg	day 21	0.5
SA240851	C18-26-pos	day 21	0.5
SA240852	HILIC-26-pos	day 21	0.5
SA240853	HILIC-26-neg	day 21	0.5
SA240854	C18-26-neg	day 21	0.5
SA240855	C18-24-neg	day 21	1.0
SA240856	C18-24-pos	day 21	1.0
SA240857	C18-27-neg	day 21	1.0
SA240858	C18-27-pos	day 21	1.0
SA240859	HILIC-24-pos	day 21	1.0
SA240860	HILIC-24-neg	day 21	1.0
SA240861	HILIC-27-pos	day 21	1.0
SA240862	HILIC-27-neg	day 21	1.0
SA240863	C18-1-pos	day 7	0.0
SA240864	C18-7-pos	day 7	0.0
SA240865	C18-1-neg	day 7	0.0
SA240866	HILIC-1-pos	day 7	0.0
SA240867	HILIC-7-pos	day 7	0.0
SA240868	HILIC-4-pos	day 7	0.0
SA240869	C18-4-pos	day 7	0.0
SA240870	HILIC-4-neg	day 7	0.0
SA240871	HILIC-7-neg	day 7	0.0
SA240872	C18-7-neg	day 7	0.0
SA240873	C18-4-neg	day 7	0.0
SA240874	HILIC-1-neg	day 7	0.0
SA240875	C18-2-pos	day 7	0.5
SA240876	C18-5-pos	day 7	0.5
SA240877	C18-8-neg	day 7	0.5
SA240878	C18-5-neg	day 7	0.5
SA240879	HILIC-5-pos	day 7	0.5
SA240880	HILIC-5-neg	day 7	0.5
SA240881	HILIC-8-pos	day 7	0.5
SA240882	C18-8-pos	day 7	0.5
SA240883	C18-2-neg	day 7	0.5
SA240884	HILIC-8-neg	day 7	0.5
SA240885	HILIC-2-pos	day 7	0.5
SA240886	HILIC-2-neg	day 7	0.5
SA240887	C18-6-pos	day 7	1.0
SA240888	C18-6-neg	day 7	1.0

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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