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.

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Study IDST003041
Study TitleSoil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats
Study SummaryThis 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 NameRodić
First NameNebojša
AddressStepe Stepanovića 5, Čonoplja, Vojvodina, Serbia
Emailnebojsa.rodic@hotmail.com
Phone+381648766400
Submit Date2024-01-05
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-01-16
Release Version1
Nebojša Rodić Nebojša Rodić
https://dx.doi.org/10.21228/M8VX1B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

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
SA330265EV_A1A flowering neutral G1
SA330266EV_A4A flowering neutral G1
SA330267EV_A5A flowering neutral G1
SA330268EV_A3A flowering neutral G1
SA330269EV_A2A flowering neutral G1
SA330270EV_AVIIA rosette neutral G1
SA330271EV_AVIIIA rosette neutral G1
SA330272EV_AVIA rosette neutral G1
SA330273EV_AIVA rosette neutral G1
SA330274EV_AIA rosette neutral G1
SA330275EV_AVA rosette neutral G1
SA330276EV_AIIA rosette neutral G1
SA330277EV_B6B flowering neutral G1
SA330278EV_B4B flowering neutral G1
SA330279EV_B5B flowering neutral G1
SA330280EV_B1B flowering neutral G1
SA330281EV_B2B flowering neutral G1
SA330282EV_B3B flowering neutral G1
SA330283EV_BVIB rosette neutral G1
SA330284EV_BVB rosette neutral G1
SA330285EV_BIVB rosette neutral G1
SA330286EV_BIB rosette neutral G1
SA330287EV_BIIB rosette neutral G1
SA330288EV_BIIIB rosette neutral G1
SA330289EV_C6C flowering neutral G2
SA330290EV_C5C flowering neutral G2
SA330291EV_C1C flowering neutral G2
SA330292EV_C4C flowering neutral G2
SA330293EV_C2C flowering neutral G2
SA330294EV_C3C flowering neutral G2
SA330295EV_CVC rosette neutral G2
SA330296EV_CVIC rosette neutral G2
SA330297EV_CIIIC rosette neutral G2
SA330298EV_CIVC rosette neutral G2
SA330299EV_CIC rosette neutral G2
SA330300EV_CIIC rosette neutral G2
SA330301EV_EVIE rosette slightly alkaline G2
SA330302EV_EVE rosette slightly alkaline G2
SA330303EV_EIVE rosette slightly alkaline G2
SA330304EV_EIE rosette slightly alkaline G2
SA330305EV_EIIE rosette slightly alkaline G2
SA330306EV_EIIIE rosette slightly alkaline G2
SA330307EV_F6F flowering slightly alkaline G2
SA330308EV_F5F flowering slightly alkaline G2
SA330309EV_F1F flowering slightly alkaline G2
SA330310EV_F4F flowering slightly alkaline G2
SA330311EV_F2F flowering slightly alkaline G2
SA330312EV_F3F flowering slightly alkaline G2
SA330313EV_FVIF rosette slightly alkaline G2
SA330314EV_FVF rosette slightly alkaline G2
SA330315EV_FIIF rosette slightly alkaline G2
SA330316EV_FIVF rosette slightly alkaline G2
SA330317EV_FIF rosette slightly alkaline G2
SA330318EV_FIIIF rosette slightly alkaline G2
SA330319EV_GVIG rosette moderately acidic G2
SA330320EV_GVIIG rosette moderately acidic G2
SA330321EV_GVG rosette moderately acidic G2
SA330322EV_GIG rosette moderately acidic G2
SA330323EV_GIVG rosette moderately acidic G2
SA330324EV_GIIG rosette moderately acidic G2
SA330325EV_GIIIG rosette moderately acidic G2
SA330326QC_EVNA NA NA NA
SA330327QC_EV_02NA NA NA NA
SA330328QC_EV_03NA 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
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