Summary of Study ST003041
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 PR001283. The data can be accessed directly via it's Project DOI: 10.21228/M8VX1B 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 | ST003041 |
| Study Title | Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats |
| Study Summary | This study examines the impact of different factors (geographic location, soil pH, genetic cluster, developmental stage) on the metabolome and microbiome of wild Echium vulgare, as well as the microbiome-metabolome correlation contained therein. Samples analyzed are wild Echium vulgare plant roots collected at six locations in Austria; out of the six locations, four contain plant roots from two different developmental stages. Extraction of metabolites and subsequent UHPLC-HRMS analysis were performed to obtain data for metabolomics analysis. |
| Institute | Aristotle University of Thessaloniki |
| Last Name | Rodić |
| First Name | Nebojša |
| Address | Stepe Stepanovića 5, Čonoplja, Vojvodina, Serbia |
| nebojsa.rodic@hotmail.com | |
| Phone | +381648766400 |
| Submit Date | 2024-01-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-01-16 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001283 |
| Project DOI: | doi: 10.21228/M8VX1B |
| Project Title: | MICROMETABOLITE |
| Project Summary: | The overall objective of MICROMETABOLITE is to explore interactions between plants and microorganisms involved in the production of secondary metabolites (SM) for introducing novel ingredients in pharmaceutical and cosmeceutical industry. Effects of microorganisms on the plant metabolome and the biosynthesis of bioactive SM will be studied in the Boraginaceae plant family, aimed at optimising plant cultivation and alkannins/shikonins (A/S) production. Microorganisms will be integrated in plant production systems, and protocols needed for efficient implementation in industry will be elaborated. Thereby a platform will be established that will support long-term interactions between academia and industry. |
| Institute: | Aristotle University of Thessaloniki |
| Department: | School of Chemical Engineering |
| Laboratory: | Organic Chemistry Laboratory |
| Last Name: | Rodic |
| First Name: | Nebojsa |
| Address: | Stepe Stepanovica 5, Conoplja, Vojvodina, 25210, Serbia |
| Email: | nebojsa.rodic@hotmail.com |
| Phone: | +381648766400 |
| Funding Source: | This research was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 721635 |
Subject:
| Subject ID: | SU003155 |
| Subject Type: | Plant |
| Subject Species: | Echium vulgare |
| Species Group: | Plants |
Factors:
Subject type: Plant; Subject species: Echium vulgare (Factor headings shown in green)
| mb_sample_id | local_sample_id | Location | Developmental Stage | Soil pH | Genetic cluster |
|---|---|---|---|---|---|
| SA330265 | EV_A1 | A | flowering | neutral | G1 |
| SA330266 | EV_A4 | A | flowering | neutral | G1 |
| SA330267 | EV_A5 | A | flowering | neutral | G1 |
| SA330268 | EV_A3 | A | flowering | neutral | G1 |
| SA330269 | EV_A2 | A | flowering | neutral | G1 |
| SA330270 | EV_AVII | A | rosette | neutral | G1 |
| SA330271 | EV_AVIII | A | rosette | neutral | G1 |
| SA330272 | EV_AVI | A | rosette | neutral | G1 |
| SA330273 | EV_AIV | A | rosette | neutral | G1 |
| SA330274 | EV_AI | A | rosette | neutral | G1 |
| SA330275 | EV_AV | A | rosette | neutral | G1 |
| SA330276 | EV_AII | A | rosette | neutral | G1 |
| SA330277 | EV_B6 | B | flowering | neutral | G1 |
| SA330278 | EV_B4 | B | flowering | neutral | G1 |
| SA330279 | EV_B5 | B | flowering | neutral | G1 |
| SA330280 | EV_B1 | B | flowering | neutral | G1 |
| SA330281 | EV_B2 | B | flowering | neutral | G1 |
| SA330282 | EV_B3 | B | flowering | neutral | G1 |
| SA330283 | EV_BVI | B | rosette | neutral | G1 |
| SA330284 | EV_BV | B | rosette | neutral | G1 |
| SA330285 | EV_BIV | B | rosette | neutral | G1 |
| SA330286 | EV_BI | B | rosette | neutral | G1 |
| SA330287 | EV_BII | B | rosette | neutral | G1 |
| SA330288 | EV_BIII | B | rosette | neutral | G1 |
| SA330289 | EV_C6 | C | flowering | neutral | G2 |
| SA330290 | EV_C5 | C | flowering | neutral | G2 |
| SA330291 | EV_C1 | C | flowering | neutral | G2 |
| SA330292 | EV_C4 | C | flowering | neutral | G2 |
| SA330293 | EV_C2 | C | flowering | neutral | G2 |
| SA330294 | EV_C3 | C | flowering | neutral | G2 |
| SA330295 | EV_CV | C | rosette | neutral | G2 |
| SA330296 | EV_CVI | C | rosette | neutral | G2 |
| SA330297 | EV_CIII | C | rosette | neutral | G2 |
| SA330298 | EV_CIV | C | rosette | neutral | G2 |
| SA330299 | EV_CI | C | rosette | neutral | G2 |
| SA330300 | EV_CII | C | rosette | neutral | G2 |
| SA330301 | EV_EVI | E | rosette | slightly alkaline | G2 |
| SA330302 | EV_EV | E | rosette | slightly alkaline | G2 |
| SA330303 | EV_EIV | E | rosette | slightly alkaline | G2 |
| SA330304 | EV_EI | E | rosette | slightly alkaline | G2 |
| SA330305 | EV_EII | E | rosette | slightly alkaline | G2 |
| SA330306 | EV_EIII | E | rosette | slightly alkaline | G2 |
| SA330307 | EV_F6 | F | flowering | slightly alkaline | G2 |
| SA330308 | EV_F5 | F | flowering | slightly alkaline | G2 |
| SA330309 | EV_F1 | F | flowering | slightly alkaline | G2 |
| SA330310 | EV_F4 | F | flowering | slightly alkaline | G2 |
| SA330311 | EV_F2 | F | flowering | slightly alkaline | G2 |
| SA330312 | EV_F3 | F | flowering | slightly alkaline | G2 |
| SA330313 | EV_FVI | F | rosette | slightly alkaline | G2 |
| SA330314 | EV_FV | F | rosette | slightly alkaline | G2 |
| SA330315 | EV_FII | F | rosette | slightly alkaline | G2 |
| SA330316 | EV_FIV | F | rosette | slightly alkaline | G2 |
| SA330317 | EV_FI | F | rosette | slightly alkaline | G2 |
| SA330318 | EV_FIII | F | rosette | slightly alkaline | G2 |
| SA330319 | EV_GVI | G | rosette | moderately acidic | G2 |
| SA330320 | EV_GVII | G | rosette | moderately acidic | G2 |
| SA330321 | EV_GV | G | rosette | moderately acidic | G2 |
| SA330322 | EV_GI | G | rosette | moderately acidic | G2 |
| SA330323 | EV_GIV | G | rosette | moderately acidic | G2 |
| SA330324 | EV_GII | G | rosette | moderately acidic | G2 |
| SA330325 | EV_GIII | G | rosette | moderately acidic | G2 |
| SA330326 | QC_EV | NA | NA | NA | NA |
| SA330327 | QC_EV_02 | NA | NA | NA | NA |
| SA330328 | QC_EV_03 | NA | NA | NA | NA |
| Showing results 1 to 64 of 64 |
Collection:
| Collection ID: | CO003148 |
| Collection Summary: | Echium vulgare plants were collected in six locations in Austria. Four of the locations contained both rosette-stage and flowering plants, while two of the remaining locations contained only rosette-stage plants. Roots of the plants were collected and subsequently analyzed. |
| Sample Type: | Plant roots |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003164 |
| Treatment Summary: | After the collection, no additional treatment except for the cutting of roots was performed. The roots were split into parts for various microbiological analyses and parts for metabolomics analysis. |
Sample Preparation:
| Sampleprep ID: | SP003161 |
| Sampleprep Summary: | Plant roots were ground to a fine powder using a ball mill (Fritsch Pulverisette 0, Germany). Each powdered sample was weighed (70 mg) into microcentrifuge tubes, followed by extraction with 3 mL of methanol by ultrasound at 10% power for 3 h (Bandelin Sonorex Digital 10P, Berlin, Germany) and centrifugation for 10 minutes at 12.500 rpm (Hermle Z 216 MK, Wehingen, Germany). The supernatants were collected and subjected to UHPLC-HRMS analysis after filtering with 0.22 μm syringe filters. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | Room temperature |
Combined analysis:
| Analysis ID | AN004988 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Accela AS |
| Column | Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo LTQ Discovery Orbitrap |
| Ion Mode | POSITIVE |
| Units | Intensity |
Chromatography:
| Chromatography ID: | CH003768 |
| Instrument Name: | Thermo Accela AS |
| Column Name: | Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0 min 95A/5B, 1 min 50A/50B, 8 min 0A/100B, 13 min 0A/100B, 13.01 min 95A/5B, 16 min 95A/5B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | Ultrapure water (0.1% formic acid) |
| Solvent B: | LCMS-grade methanol (0.1% formic acid) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004728 |
| Analysis ID: | AN004988 |
| Instrument Name: | Thermo LTQ Discovery Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The MS/MS data were obtained for the six most intense m/z peaks in each full scan, with the normalized collision energy set to 35 eV. The acquisition and initial processing of the data were by means of XcaliburTM (Thermo Scientific, USA) software, while data alignment and feature extraction were performed utilizing the XCMS Online platform (The Scripps Research Institute, USA). |
| Ion Mode: | POSITIVE |
