Summary of Study ST003307
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 PR002057. The data can be accessed directly via it's Project DOI: 10.21228/M8QN7M 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 | ST003307 |
| Study Title | Untargeted metabolomics of rhizosphere soil from 4-years Panax ginseng that was treated with endo-borneol under field condition |
| Study Summary | To study the rhizosphere soil matabolism of 4-years Panax ginseng that were leaf-sprayed with endo-borneol at different concentrations (0, 0.1 mg/L, and 100 mg/L) under field condition, liquid chromarography tandem mass spectrometry was used for examination. Each treatment is set with 6 replicates for assessing nontargeted metabolomics. The LC-MS/MS analysis was performed using a Thermo UHPLC-Q Exactive HF-X system equipped with an ACQUITY HSS T3 column. As a result, a total of 296 and 569 metabolites were identified in negative ion mode and positive mode, respectively. |
| Institute | Yunnan University |
| Department | School of Agriculture |
| Laboratory | Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China |
| Last Name | Xing-Yu |
| First Name | Ji |
| Address | Road Fengyuan, District Panlong, Kunming, Yunnan, China |
| xingyu.ji@hotmail.com | |
| Phone | ＋86-13354989110 |
| Submit Date | 2024-06-03 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002057 |
| Project DOI: | doi: 10.21228/M8QN7M |
| Project Title: | Use of untargeted metabolomics for assessing soil from Panax ginseng that were leaf-sprayed with endo-borneol |
| Project Summary: | To study the rhizosphere soil matabolism of 4-years Panax ginseng that wereleaf-sprayed with endo-borneol at different concentrations (0, 0.1 mg/L, and 100 mg/L) under field condition, liquid chromarography tandem mass spectrometry was used for examination. Each treatment is set with 6 replicates for assessing nontargeted metabolomics. The LC-MS/MS analysis was performed using a Thermo UHPLC-Q Exactive HF-X system equipped with an ACQUITY HSS T3 column. As a result, a total of 296 and 569 metabolites were identified in negative ion mode and positive mode, respectively. |
| Institute: | Yunnan University |
| Department: | School of Agriculture |
| Laboratory: | State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan |
| Last Name: | Ji |
| First Name: | Xing-Yu |
| Address: | Yuhua Road, Chenggong, Kunming, Yunnan Province, 650100, China |
| Email: | xingyu.ji@hotmail.com |
| Phone: | ＋86-13354989110 |
| Funding Source: | Natural Science Foundation of China |
| Project Comments: | U23A20202 |
| Publications: | still under review |
| Contributors: | Xing-Yu Ji, Shusheng Zhu |
Subject:
| Subject ID: | SU003428 |
| Subject Type: | Soil sample |
Factors:
Subject type: Soil sample; Subject species: - (Factor headings shown in green)
| mb_sample_id | local_sample_id | endo-borneol concentration |
|---|---|---|
| SA358673 | CK_2_neg | 0 |
| SA358674 | CK_4_neg | 0 |
| SA358675 | CK_3_neg | 0 |
| SA358676 | CK_1_pos | 0 |
| SA358677 | CK_2_pos | 0 |
| SA358678 | CK_4_pos | 0 |
| SA358679 | CK_3_pos | 0 |
| SA358680 | CK_1_neg | 0 |
| SA358657 | T3_6_pos | 0.1 mg/L |
| SA358658 | CK_5_neg | 0.1 mg/L |
| SA358659 | CK_6_neg | 0.1 mg/L |
| SA358660 | T3_1_neg | 0.1 mg/L |
| SA358661 | T3_2_neg | 0.1 mg/L |
| SA358662 | T3_3_neg | 0.1 mg/L |
| SA358663 | T3_4_neg | 0.1 mg/L |
| SA358664 | T3_5_pos | 0.1 mg/L |
| SA358665 | T3_4_pos | 0.1 mg/L |
| SA358666 | T3_3_pos | 0.1 mg/L |
| SA358667 | T3_2_pos | 0.1 mg/L |
| SA358668 | T3_1_pos | 0.1 mg/L |
| SA358669 | CK_6_pos | 0.1 mg/L |
| SA358670 | CK_5_pos | 0.1 mg/L |
| SA358671 | T3_5_neg | 0.1 mg/L |
| SA358672 | T3_6_neg | 0.1 mg/L |
| SA358681 | T7_6_pos | 100 mg/L |
| SA358682 | T7_6_neg | 100 mg/L |
| SA358683 | T7_5_neg | 100 mg/L |
| SA358684 | T7_4_neg | 100 mg/L |
| SA358685 | T7_3_neg | 100 mg/L |
| SA358686 | T7_2_neg | 100 mg/L |
| SA358687 | T7_1_neg | 100 mg/L |
| SA358688 | T7_1_pos | 100 mg/L |
| SA358689 | T7_2_pos | 100 mg/L |
| SA358690 | T7_3_pos | 100 mg/L |
| SA358691 | T7_4_pos | 100 mg/L |
| SA358692 | T7_5_pos | 100 mg/L |
| SA358693 | QC3_pos | QC |
| SA358694 | QC2_pos | QC |
| SA358695 | QC1_neg | QC |
| SA358696 | QC2_neg | QC |
| SA358697 | QC3_neg | QC |
| SA358698 | QC1_pos | QC |
| Showing results 1 to 42 of 42 |
Collection:
| Collection ID: | CO003421 |
| Collection Summary: | Rhizosphere soil samples were collected from Panax ginseng that were leaf sprayed with endo-borneol at 0, 0.1, 100 mg/L. The samples were snap-frozen using liquid nitrogen and stored in -80°C for metabolism analysis. |
| Sample Type: | Soil |
| Collection Method: | Gently brushed from the roots of Panax ginseng |
| Collection Location: | Laobiangou, County Benxi, Liaoning, China |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003437 |
| Treatment Summary: | Panax ginseng were leaf sprayed with endo-borneol at 0, 0.1, 100 mg/L from July to August, 2021. Six replicates were set for each group as six plots.Then the rhizosphere soil of Panax ginseng from each treatment was collected. |
Sample Preparation:
| Sampleprep ID: | SP003435 |
| Sampleprep Summary: | 50 mg solid sample was added to a 2 mL centrifuge tube and a 6 mm diameter grinding bead was added. 400 μL of extraction solution (methanol: water = 4:1 (v:v)) containing 0.02 mg/mL of internal standard (L-2-chlorophenylalanine) was used for metabolite extraction. Samples were ground by the Wonbio-96c (Shanghai wanbo biotechnology co., ltd) frozen tissue grinder for 6 min (-10°C, 50 Hz), followed by low-temperature ultrasonic extraction for 30 min (5°C, 40 kHz). The samples were left at -20°C for 30 min, centrifuged for 15 min (4°C, 13000 g), and the supernatant was transferred to the injection vial for LC-MS/MS analysis. |
Chromatography:
| Chromatography ID: | CH004108 |
| Instrument Name: | Thermo Vanquish Horizon |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0-3 min: 0-20% B, 3-9 min: 20-60% B, 9-11 min: 60-100% B, maintain for 2.5 min, 13.5-13.6 min: 100% to 0% B, maintain for 2.4 min |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 95% water/5% acetonitrile; 0.1% formic acid |
| Solvent B: | 47.5% acetonitrile/47.5% isopropanol/5% water; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN005418 |
| Analysis Type: | MS |
| Chromatography ID: | CH004108 |
| Num Factors: | 4 |
| Num Metabolites: | 568 |
| Units: | Peak area |
| Analysis ID: | AN005419 |
| Analysis Type: | MS |
| Chromatography ID: | CH004108 |
| Num Factors: | 4 |
| Num Metabolites: | 295 |
| Rt Units: | Minutes |
| Units: | Peak area |
