NMR spectra of oilseed rape (Brassica napus) root exudates

SND-ID: 2023-258. Version: 1. DOI: https://doi.org/10.5878/8t82-d090

Citation

Creator/Principal investigator(s)

Elin Alexandersson - Swedish University of Agricultural Sciences, Department of Molecular Sciences orcid

Hanna Eriksson Röhnisch - Swedish University of Agricultural Sciences, Department of Molecular Sciences orcid

Research principal

Swedish University of Agricultural Sciences - Department of Molecular Sciences rorId

Principal's reference number

SLU.molsci.2023.IÄ.4.4-13

Description

The dataset contains 1D and 2D NMR spectra of root exudates from various varieties of oilseed rape (Brassica napus). A Bruker Avance III 600 MHz spectrometer connected to Topspin version 3.5 was used to record the spectra.

Included are 1D-1H-NOESY, (1H,1H)-TOCSY, (1H,13C)-HSQC, CPMG, and 1D-diffusion spectra of intact root exudates as well as 1D-1H spectra of a sample treated with ultrafiltration and solid phase extraction (SPE), respectively. The dataset further includes spectra from a spike-in experiment where different concentrations of five metabolites were added to a pooled root exudate sample as well as a blank sample. All samples have been freeze-dried and dissolved in D2O.

The data was used to develop an automated targeted metabolomics workflow called extended AQuA.

Data contains personal data

No

Language

Method and outcome

Time period(s) investigated

2021-03 – 2022-05

Data format / data structure

Species and taxons

Brassica napus

Data collection
  • Mode of collection: Laboratory experiment
  • Description of the mode of collection:
    Surface sterilised oilseed rape seeds were germinated 3-5 days on petri dishes containing 0.5× Murashige-Skoog medium (including vitamins) and 0.6% bacto agar. Plantlets (n = 8) were then transferred to 50 ml plastic tubes filled with autoclaved MilliQ water, so that the seedling roots were immersed into the water (see photo). Root exudates were then collected for four days after which they were freeze dried. Blank samples did not contain any seedlings but were otherwise treated the same.

    Lyophilised root exudate samples were dissolved in a few millilitres of MilliQ water, transferred to 15 ml plastic tubes, and dried in a vacuum centrifuge. NMR samples were prepared by adding 750 μl KH2PO4 buffer in D2O (45 mM, pD 7.0 (apparent pH 6.6)+DSS-d6 to each sample. The samples were then centrifuged for 10 min at 17000xg. For each sample, 600 µl supernatant was added to a 5 mm NMR tube.

    NMR experiments:
    - 1D-1H-NOESY, (1H,1H)-TOCSY, (1H,13C)-HSQC, CPMG, and 1D-diffusion NMR spectra were recorded of intact root exudates.
    - 1D-1H spectra of a sample treated with ultrafiltration and solid phase extraction (SPE), respectively.
    - 1D-1H spectra from a spike-in experiment where different concentrations of five metabolites were added to a pooled root exudate sample as well as a blank sample.
  • Time period(s) for data collection: 2021-03 – 2022-05
  • Data collector: Swedish University of Agricultural Sciences
  • Instrument: NMR spectrometer - Bruker Avance III 600 MHz spectrometer (5 mm 1H/13C/15N/31P inverse detection cryoprobe equipped with a z gradient) connected to Topspin version 3.5
  • Source of the data: Biological samples
Geographic coverage
Administrative information

Responsible department/unit

Department of Molecular Sciences

Contributor(s)

Corine Sandström - Swedish University of Agricultural Sciences, Department of Molecular Sciences

Johan Meijer - Swedish University of Agricultural Sciences, Department of Plant Biology

Gustav Nestor - Swedish University of Agricultural Sciences, Department of Molecular Sciences

Anders Broberg - Swedish University of Agricultural Sciences, Department of Molecular Sciences

Topic and keywords

Research area

Organic chemistry (Standard för svensk indelning av forskningsämnen 2011)

Analytical chemistry (Standard för svensk indelning av forskningsämnen 2011)

Publications

Alexandersson, E., Sandström, C., Meijer, J., Nestor, G., Broberg, A. & Röhnisch, H.E. (2024). Extended automated quantification algorithm (AQuA) for targeted 1H NMR metabolomics of highly complex samples: application to plant root exudates. Metabolomics, 20 (1), 11.
DOI: https://doi.org/10.1007/s11306-023-02073-z

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

License

CC BY 4.0

Versions

Version 1. 2024-02-09

Version 1: 2024-02-09

DOI: https://doi.org/10.5878/8t82-d090

Contacts for questions about the data

Elin Alexandersson

elin.alexandersson@slu.se

Hanna Eriksson Röhnisch

hanna.eriksson.rohnisch@slu.se

SLU Arkiv

arkiv@slu.se

Published: 2024-02-09