Summary of Study ST002012

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 PR001276. The data can be accessed directly via it's Project DOI: 10.21228/M8S70F This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST002012
Study Title	Untargeted primary metabolite profiling in Arabidopsis thaliana
Study Summary	The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
Institute	Salk Institute for Biological Studies
Department	PBIO
Laboratory	Joanne Chory
Last Name	Wu
First Name	Xuelin
Address	Salk Institute for Biological Studies
Email	xwu@salk.edu
Phone	858-453-4100, x1128
Submit Date	2021-12-09
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2022-01-02
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001276
Project DOI:	doi: 10.21228/M8S70F
Project Title:	Untargeted primary metabolite profiling in Arabidopsis thaliana
Project Summary:	The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
Institute:	Salk Institute for Biological Studies
Department:	PBIO
Laboratory:	Joanne Chory
Last Name:	Wu
First Name:	Xuelin
Address:	Salk Institute for Biological Studies
Email:	xwu@salk.edu
Phone:	+1-410-558-8510
Funding Source:	HHMI, TED Audacious Project

Subject:

Subject ID:	SU002098
Subject Type:	Plant
Subject Species:	Arabidopsis thaliana
Taxonomy ID:	3702

Factors:

Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id	local_sample_id	organ	genotype
SA188985	8_008	inflourescences	12-6_F
SA188986	7_007	inflourescences	12-6_F
SA188987	9_009	inflourescences	12-6_F
SA188988	10_010	inflourescences	12-6_F
SA188989	11_011	inflourescences	12-6_F
SA188990	12_012	inflourescences	12-6_F
SA188991	30_030	inflourescences	18-4_F
SA188992	28_028	inflourescences	18-4_F
SA188993	25_025	inflourescences	18-4_F
SA188994	26_026	inflourescences	18-4_F
SA188995	27_027	inflourescences	18-4_F
SA188996	29_029	inflourescences	18-4_F
SA188997	48_048	inflourescences	290_F
SA188998	43_043	inflourescences	290_F
SA188999	44_044	inflourescences	290_F
SA189000	45_045	inflourescences	290_F
SA189001	46_046	inflourescences	290_F
SA189002	47_047	inflourescences	290_F
SA189003	62_062	inflourescences	Col-0_F
SA189004	65_065	inflourescences	Col-0_F
SA189005	66_066	inflourescences	Col-0_F
SA189006	63_063	inflourescences	Col-0_F
SA189007	64_064	inflourescences	Col-0_F
SA189008	61_061	inflourescences	Col-0_F
SA189009	17_017	leaves	12-6_L
SA189010	16_016	leaves	12-6_L
SA189011	18_018	leaves	12-6_L
SA189012	15_015	leaves	12-6_L
SA189013	13_013	leaves	12-6_L
SA189014	14_014	leaves	12-6_L
SA189015	35_035	leaves	18-4_L
SA189016	36_036	leaves	18-4_L
SA189017	34_034	leaves	18-4_L
SA189018	33_033	leaves	18-4_L
SA189019	31_031	leaves	18-4_L
SA189020	32_032	leaves	18-4_L
SA189021	54_054	leaves	290_L
SA189022	53_053	leaves	290_L
SA189023	49_049	leaves	290_L
SA189024	52_052	leaves	290_L
SA189025	50_050	leaves	290_L
SA189026	51_051	leaves	290_L
SA189027	71_071	leaves	Col-0_L
SA189028	72_072	leaves	Col-0_L
SA189029	70_070	leaves	Col-0_L
SA189030	69_069	leaves	Col-0_L
SA189031	67_067	leaves	Col-0_L
SA189032	68_068	leaves	Col-0_L
SA189033	4_004	roots	12-6_R
SA189034	6_006	roots	12-6_R
SA189035	5_005	roots	12-6_R
SA189036	3_003	roots	12-6_R
SA189037	2_002	roots	12-6_R
SA189038	1_001	roots	12-6_R
SA189039	23_023	roots	18-4_R
SA189040	20_020	roots	18-4_R
SA189041	24_024	roots	18-4_R
SA189042	19_019	roots	18-4_R
SA189043	22_022	roots	18-4_R
SA189044	21_021	roots	18-4_R
SA189045	42_042	roots	290_R
SA189046	41_041	roots	290_R
SA189047	38_038	roots	290_R
SA189048	40_040	roots	290_R
SA189049	37_037	roots	290_R
SA189050	39_039	roots	290_R
SA189051	59_059	roots	Col-0_R
SA189052	60_060	roots	Col-0_R
SA189053	57_057	roots	Col-0_R
SA189054	55_055	roots	Col-0_R
SA189055	56_056	roots	Col-0_R
SA189056	58_058	roots	Col-0_R

Showing results 1 to 72 of 72

Showing results 1 to 72 of 72

Collection:

Collection ID:	CO002091
Collection Summary:	Samples were collected from live plants and frozen in liquid nitrogen
Sample Type:	Plant

Treatment:

Treatment ID:	TR002110
Treatment Summary:	four genotypes, each with three tissue types, 6, no treatment, just genotype and tissue type difference.

Sample Preparation:

Sampleprep ID:	SP002104
Sampleprep Summary:	Extraction of Plant Samples: Leaves 1. References: Fiehn O (2006) Metabolite Profiling in Arabidopsis. In: Arabidopsis Protocols 2nd edition. Salinas J, Sanchez-Serrano JJ (eds.), Methods in Molecular Biology ser., Humana Press, Totowa NJ, 439-447 Weckwerth W, Wenzel K, Fiehn O (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83 2. Starting material: Arabidopsis rosette leaves: 20±5 mg fresh weight sample OR 2 mg dry weight sample Rice leaves: 10±3 mg fresh weight sample OR 1 mg dry weight sample Other plant organs not validated but advised to use this SOP in a similar manner 3. Equipment: Eppendorf pipettes: 1-200µL and 100-1000µL Eppendorf tubes 2.0mL, uncoloured (Cat. No. 022363204 ) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Precision balance with accuracy ± 0.1 mg ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer, VWR. Speed vacuum concentration system (Labconco Centrivap cold trap) Ball mill MM301 (Retsch corp.) Metal balls (Retsch 3 mm I.D. Cat. No 22.455.0002 or 5 mm I.D. Cat. No 22.455.0003) Large tweezers Dewar cold gloves 2 liquid nitrogen dewars pH paper 5-10 (EMD Chem. Inc.) Crushed ice Nitrogen line with pipette tip Cork borer (Ø diameter of cylinder related to the amount to be used. 4 mm I.D. for Arabidopsis leaves.) 4. Chemicals Methanol, LCMS grade Chloroform, HPLC grade Liquid nitrogen Water, Millipore (pure) 5. Harvest Procedure NOTE: No weighing of plant material needed unless the experimental design suggests marked changes for the ratio of leaf disk diameter to fresh weight, e.g. in drought stress experiments. In such cases, leaves need to be lyophilized and weighed prior to extraction Label Eppendorf tubes according to the sample name defined in SetupX and put a grinding ball in each. Using the cork borer take one or two disks per leaf and immediately transfer to an Eppendorf tube. Close the tube and immediately place into the dewar of liquid nitrogen. 6. Preparation of extraction mix and material Check the pH of methanol (pH7) Switch on the ThermoElectron Neslab RTE 740 cooling bath at to pre-cool at –18°C to -22°C Make the extraction solution by mixing methanol, chloroform, and water in proportions of 5 : 2 : 2 Rinse the extraction solution for 5 min with nitrogen, making sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution. 7. Homogenisation and extraction Take the Eppendorf tubes from the liquid nitrogen and place into the tube-holder of the grinder being careful to compensate for weight, maintaining equilibrium. Shake for 30s at a frequency of 25 s-1 and check that the leaves have been ground into a fine powder. Repeat if necessary, submerging in liquid nitrogen first. After grinding add 1mL of pre-chilled extraction solution to each tube one by one to prevent even partial thawing of the sample. Store all samples on ice while finishing this step. Vortex the sample for 10s and shake on the Orbital Mixing Chilling/Heating Plate for 6 minutes at 4°C Centrifuge for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. Remove the whole supernatant in two 500uL portions, saving one as a backup. Dry one portion in the Labconco Centrivap cold trap concentrator to complete dryness and submit for derivitization. 8. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 8. Quality assurance For each sequence perform one blank negative control by applying the total procedure (i.e. all materials and plastic ware) without biological sample. Also perform all tasks once samples/standards have come to room temperature. Finally, include a pure MSTFA vial for liner conditioning steps. 9. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Sampleprep ID:

SP002104

Sampleprep Summary:

Extraction of Plant Samples: Leaves 1. References: Fiehn O (2006) Metabolite Profiling in Arabidopsis. In: Arabidopsis Protocols 2nd edition. Salinas J, Sanchez-Serrano JJ (eds.), Methods in Molecular Biology ser., Humana Press, Totowa NJ, 439-447 Weckwerth W, Wenzel K, Fiehn O (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83 2. Starting material: Arabidopsis rosette leaves: 20±5 mg fresh weight sample OR 2 mg dry weight sample Rice leaves: 10±3 mg fresh weight sample OR 1 mg dry weight sample Other plant organs not validated but advised to use this SOP in a similar manner 3. Equipment: Eppendorf pipettes: 1-200µL and 100-1000µL Eppendorf tubes 2.0mL, uncoloured (Cat. No. 022363204 ) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Precision balance with accuracy ± 0.1 mg ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer, VWR. Speed vacuum concentration system (Labconco Centrivap cold trap) Ball mill MM301 (Retsch corp.) Metal balls (Retsch 3 mm I.D. Cat. No 22.455.0002 or 5 mm I.D. Cat. No 22.455.0003) Large tweezers Dewar cold gloves 2 liquid nitrogen dewars pH paper 5-10 (EMD Chem. Inc.) Crushed ice Nitrogen line with pipette tip Cork borer (Ø diameter of cylinder related to the amount to be used. 4 mm I.D. for Arabidopsis leaves.) 4. Chemicals Methanol, LCMS grade Chloroform, HPLC grade Liquid nitrogen Water, Millipore (pure) 5. Harvest Procedure NOTE: No weighing of plant material needed unless the experimental design suggests marked changes for the ratio of leaf disk diameter to fresh weight, e.g. in drought stress experiments. In such cases, leaves need to be lyophilized and weighed prior to extraction Label Eppendorf tubes according to the sample name defined in SetupX and put a grinding ball in each. Using the cork borer take one or two disks per leaf and immediately transfer to an Eppendorf tube. Close the tube and immediately place into the dewar of liquid nitrogen. 6. Preparation of extraction mix and material Check the pH of methanol (pH7) Switch on the ThermoElectron Neslab RTE 740 cooling bath at to pre-cool at –18°C to -22°C Make the extraction solution by mixing methanol, chloroform, and water in proportions of 5 : 2 : 2 Rinse the extraction solution for 5 min with nitrogen, making sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution. 7. Homogenisation and extraction Take the Eppendorf tubes from the liquid nitrogen and place into the tube-holder of the grinder being careful to compensate for weight, maintaining equilibrium. Shake for 30s at a frequency of 25 s-1 and check that the leaves have been ground into a fine powder. Repeat if necessary, submerging in liquid nitrogen first. After grinding add 1mL of pre-chilled extraction solution to each tube one by one to prevent even partial thawing of the sample. Store all samples on ice while finishing this step. Vortex the sample for 10s and shake on the Orbital Mixing Chilling/Heating Plate for 6 minutes at 4°C Centrifuge for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. Remove the whole supernatant in two 500uL portions, saving one as a backup. Dry one portion in the Labconco Centrivap cold trap concentrator to complete dryness and submit for derivitization. 8. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 8. Quality assurance For each sequence perform one blank negative control by applying the total procedure (i.e. all materials and plastic ware) without biological sample. Also perform all tasks once samples/standards have come to room temperature. Finally, include a pure MSTFA vial for liner conditioning steps. 9. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Combined analysis:

Analysis ID	AN003286
Analysis type	MS
Chromatography type	GC
Chromatography system	Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column	Rtx-5Sil MS
MS Type	EI
MS instrument type	GC-TOF
MS instrument name	Leco Pegasus IV TOF
Ion Mode	UNSPECIFIED
Units	normalized peak height

Chromatography:

Chromatography ID:	CH002426
Chromatography Summary:	Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.
Instrument Name:	Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column Name:	Rtx-5Sil MS
Chromatography Type:	GC

MS:

MS ID:	MS003057
Analysis ID:	AN003286
Instrument Name:	Leco Pegasus IV TOF
Instrument Type:	GC-TOF
MS Type:	EI
MS Comments:	Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.
Ion Mode:	UNSPECIFIED