Summary of Study ST001713

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 PR001097. The data can be accessed directly via it's Project DOI: 10.21228/M8WT3C This work is supported by NIH grant, U2C- DK119886.

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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.

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Study ID	ST001713
Study Title	Effects of different planting densities on the metabolism of Panax notoginseng
Study Type	Planting density experiment
Study Summary	At the moderate planting density, the primary metabolism (starch and sucrose metabolism) of the plants were significantly enhanced. However, the strong intraspecific competition at the higher planting densities resulted in stress as well as the accumulation of antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the planting at low densities with low intraspecific competition disturbed normal carbohydrate metabolism by upregulating galactose metabolism.
Institute	Yunnan Agricultural University
Department	College of Plant Protection
Laboratory	Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education
Last Name	Haijiao
First Name	Liu
Address	452 Fengyuan road, Kunming, Yunnan, China
Email	15832256149@163.com
Phone	+8615288149641
Submit Date	2021-01-25
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	GC-MS
Release Date	2022-01-25
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001097
Project DOI:	doi: 10.21228/M8WT3C
Project Title:	Study on metabolites of Panax notoginseng under different densities
Project Type:	Ms qualitative research
Project Summary:	At the moderate planting density, the primary metabolism (starch and sucrose metabolism) of the plants were significantly enhanced. However, the strong intraspecific competition at the higher planting densities resulted in stress as well as the accumulation of antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the planting at low densities with low intraspecific competition disturbed normal carbohydrate metabolism by upregulating galactose metabolism.
Institute:	Yunnan Agricultural University
Department:	Crop Protection Institute
Laboratory:	Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education
Last Name:	Liu
First Name:	haijiao
Address:	452 Fengyuan road, kunming, Yunnan, 650051, China
Email:	15832256149@163.com
Phone:	+8615288149641
Funding Source:	This work was supported by the National Key Research and Development Program of China (2017YFC1702502; 2018YFD0201100), Yunnan provincial key programs of Yunnan Eco-friendly Food International Cooperation Research Center project under grant (2019ZG00901), the Yunnan Academician Workstation of Chinese Academy of Engineering (2018IC063), the Young and Middle-aged Academic and Technical Leaders Reserve Programme in Yunnan Province (2017HB024), the Yunnan Ten Thousand Talents Plan Young & Elite Talents Project and Program for Innovative Research Team in Science and Technology in University of Yunnan Province (to Shusheng Zhu)

Subject:

Subject ID:	SU001790
Subject Type:	Plant
Subject Species:	Panax notoginseng
Taxonomy ID:	44586
Gender:	Not applicable

Factors:

Subject type: Plant; Subject species: Panax notoginseng (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA160377	10cm_1	10cm
SA160378	10cm_3	10cm
SA160379	10cm_4	10cm
SA160380	10cm_2	10cm
SA160381	15cm_2	15cm
SA160382	15cm_4	15cm
SA160383	15cm_1	15cm
SA160384	15cm_3	15cm
SA160385	20cm_2	20cm
SA160386	20cm_4	20cm
SA160387	20cm_1	20cm
SA160388	20cm_3	20cm
SA160389	30cm_3	30cm
SA160390	30cm_4	30cm
SA160391	30cm_2	30cm
SA160392	30cm_1	30cm
SA160393	8cm_2	8cm
SA160394	8cm_4	8cm
SA160395	8cm_1	8cm
SA160396	8cm_3	8cm

Showing results 1 to 20 of 20

Showing results 1 to 20 of 20

Collection:

Collection ID:	CO001783
Collection Summary:	Fresh fibrous root of Panax notoginseng were washed with sterile water and then flash-frozen in liquid N2
Sample Type:	Fibrous root

Treatment:

Treatment ID:	TR001803
Treatment Summary:	The experimental design for P. notoginseng cultivation is as follows: Each plastic basin (65×40×18 cm) contains about 40 kg natural soil, which was collected from a pine forest in Xundian Country, Yunnan, China (103.29°E, 25.51°N; altitude of 1960 m), then sieved to remove the residue of plant. The soil had the following characteristics: pH 5.17, electrical conductivity 458 μS cm-1, available potassium (K) 6.90 mg kg-1, available phosphate (P) 5.18 mg kg-1, alkali-hydrolyzable nitrogen (N) 172.38 mg kg-1 and organic matter 47830 mg kg-1. 4, 12, 15, 28, 45 healthy one-year old seedlings were planted in January 3, 2016 at a plant spacing of 30 cm, 20 cm, 15 cm, 10 cm and 8 cm, respectively. There were four repeats for each treatment, and a total of 20 plastic basins were placed in a completely randomized block design in greenhouse. The fresh fibrous root of P. notoginseng was collected in November 30, 2016.

Treatment ID:

TR001803

Treatment Summary:

The experimental design for P. notoginseng cultivation is as follows: Each plastic basin (65×40×18 cm) contains about 40 kg natural soil, which was collected from a pine forest in Xundian Country, Yunnan, China (103.29°E, 25.51°N; altitude of 1960 m), then sieved to remove the residue of plant. The soil had the following characteristics: pH 5.17, electrical conductivity 458 μS cm-1, available potassium (K) 6.90 mg kg-1, available phosphate (P) 5.18 mg kg-1, alkali-hydrolyzable nitrogen (N) 172.38 mg kg-1 and organic matter 47830 mg kg-1. 4, 12, 15, 28, 45 healthy one-year old seedlings were planted in January 3, 2016 at a plant spacing of 30 cm, 20 cm, 15 cm, 10 cm and 8 cm, respectively. There were four repeats for each treatment, and a total of 20 plastic basins were placed in a completely randomized block design in greenhouse. The fresh fibrous root of P. notoginseng was collected in November 30, 2016.

Sample Preparation:

Sampleprep ID:	SP001796
Sampleprep Summary:	Approximately 60 mg of frozen powder fibrous roots and 1 mL of methanol (CH3OH) containing 0.5 mg of ribitol were added into a prechilled 2 mL lock-cap centrifuge tube, then vortexed for 10 s. A 300 μL extraction aliquot (H2O:methanol:chloroform=1:2.5:1, v:v:v) was added and ultrasonically extracted for 30 min at 37°C. Then, the sample was centrifuged (1600 g, 3 min) to separate the polar and nonpolar phases. Then the upper polar phase was transferred to a fresh centrifuge tube and added 200 μL sterile water, and then vortexed and centrifuged (1600 g, 4°C for 3 min). A 250 μL aliquot of the upper phase was transferred to a fresh centrifuge tube, dried for 3-4 h at room temperature using a SpeedVac (Christ, Germany). Adding 80 μL of methoxyamine hydrochloride solution (20 mg mL-1 dissolved in pyridine) to each sample and incubating for 90 min at 30°C to protect carbonyl moieties. And then, 40 μL N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was added and incubating at 37°C for 30 min to trimethylsilylate the acidic protons. After this step, the sample was centrifuged (1600 g, 4°C for 3 min), then the supernatant was stored at 4°C for further analysis.

Sampleprep ID:

SP001796

Sampleprep Summary:

Approximately 60 mg of frozen powder fibrous roots and 1 mL of methanol (CH3OH) containing 0.5 mg of ribitol were added into a prechilled 2 mL lock-cap centrifuge tube, then vortexed for 10 s. A 300 μL extraction aliquot (H2O:methanol:chloroform=1:2.5:1, v:v:v) was added and ultrasonically extracted for 30 min at 37°C. Then, the sample was centrifuged (1600 g, 3 min) to separate the polar and nonpolar phases. Then the upper polar phase was transferred to a fresh centrifuge tube and added 200 μL sterile water, and then vortexed and centrifuged (1600 g, 4°C for 3 min). A 250 μL aliquot of the upper phase was transferred to a fresh centrifuge tube, dried for 3-4 h at room temperature using a SpeedVac (Christ, Germany). Adding 80 μL of methoxyamine hydrochloride solution (20 mg mL-1 dissolved in pyridine) to each sample and incubating for 90 min at 30°C to protect carbonyl moieties. And then, 40 μL N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was added and incubating at 37°C for 30 min to trimethylsilylate the acidic protons. After this step, the sample was centrifuged (1600 g, 4°C for 3 min), then the supernatant was stored at 4°C for further analysis.

Combined analysis:

Analysis ID	AN002788
Analysis type	MS
Chromatography type	GC
Chromatography system	Shimadzu GCMS-QP2010 ultra
Column	Agilent HP5-MS (30m x 0.25mm, 0.25 um)
MS Type	EI
MS instrument type	GC-TOF
MS instrument name	Shimadzu QP2010 Ultra
Ion Mode	UNSPECIFIED
Units	Peak area

Chromatography:

Chromatography ID:	CH002063
Instrument Name:	Shimadzu GCMS-QP2010 ultra
Column Name:	Agilent HP5-MS (30m x 0.25mm, 0.25 um)
Chromatography Type:	GC

MS:

MS ID:	MS002584
Analysis ID:	AN002788
Instrument Name:	Shimadzu QP2010 Ultra
Instrument Type:	GC-TOF
MS Type:	EI
MS Comments:	Mass spectra were obtained in electron impact (EI) ionization mode at 70 eV by monitoring the full-scan range (m/z 45-600);the raw peak obtained by data baseline filtering and calibration, peak alignment, deconvolution analysis and peak identification using MS-DIAL with the Fiehn library. The peak areas of metabolites in raw MS-Dial output (Supplementary Table S2) were normalization by sum, transformation by log and scaling by Pareto method on Metaboanalyst 4.0 (http://www.metaboanalyst.ca/MetaboAnalyst/)
Ion Mode:	UNSPECIFIED