Summary of study ST000889

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 PR000618. The data can be accessed directly via it's Project DOI: 10.21228/M8SH53 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 IDST000889
Study TitleGC-MS analysis of Quercus ilex organs (leaves, roots and acorns)
Study TypeUntargeted metabolomics
Study SummaryQualitative metabolomics study on leaves, roots and acorns from Quercus ilex plantlets. We analyzed polar(metanol:water) and apolar (chloroform) fractions.
Institute
Universidad de Córdoba
DepartmentDepartment Biochemistry and Molecular Biology
LaboratoryAgroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last NameLópez-Hidalgo
First NameCristina
AddressCampus de Rabanales; Edificio C6, Planta Baja
Emailn12lohic@uco.es
Phone626894948
Submit Date2017-10-10
Raw Data AvailableYes
Raw Data File Type(s).rar
Analysis Type DetailGC-MS
Release Date2018-06-05
Release Version1
Cristina López-Hidalgo Cristina López-Hidalgo
https://dx.doi.org/10.21228/M8SH53
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000618
Project DOI:doi: 10.21228/M8SH53
Project Title:GC-MS Quercus ilex analysis
Project Type:MS qualitative analysis
Project Summary:GC-MS analysis of samples from Quercus ilex. The objetive of the study is to obtain a better understanding of the molecular mechanisms mediating phenotypes of interest and the selection of elite genotypes to be used in restoration and reforestation programs, especially in a future climate change scenario.
Institute:Universidad de Córdoba
Department:Department Biochemistry and Molecular Biology
Laboratory:Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last Name:López-Hidalgo
First Name:Cristina
Address:Campus de Rabanales; Edificio C6, Planta Baja
Email:n12lohic@uco.es
Phone:626894948
Funding Source:This work was supported by the University of Cordoba and financial support from the Spanish Ministry of Economy and Competitiveness (Project BIO2015-64737-R2).
Publications:Metabolic network reconstruction from multi-omics data integration in Quercus ilex

Subject:

Subject ID:SU000926
Subject Type:Plant
Subject Species:Quercus ilex
Taxonomy ID:58334
Species Group:Plant

Factors:

Subject type: Plant; Subject species: Quercus ilex (Factor headings shown in green)

mb_sample_id local_sample_id Sample Type
SA052409Acorn1Acorn
SA052410Acorn3Acorn
SA052411Acorn2Acorn
SA052412Leaf3Leaf
SA052413Leaf2Leaf
SA052414Leaf1Leaf
SA052415Root3Root
SA052416Root2Root
SA052417Root1Root
Showing results 1 to 9 of 9

Collection:

Collection ID:CO000920
Collection Summary:Germinated embryo, leaves and roots from four-months plantlets were collected separately, weighted and individually frozen in liquid nitrogen.
Sample Type:Plant

Treatment:

Treatment ID:TR000940
Treatment Summary:Mature acorns from Holm oak (Quercus ilex L. subsp. ballota [Desf.] Samp.) were collected from a tree located in Aldea de Cuenca (province of Córdoba, Andalusia, Spain). Acorns were germinated and seedlings grew in a chamber under controlled conditions (a 12h photoperiod, a temperature of 21± 1ºC, a relative humidity of 60 ± 5% and an irradiance of 200 µmol m-2 s-1, Echevarría-Zomeño et al., 2009).

Sample Preparation:

Sampleprep ID:SP000933
Sampleprep Summary:Metabolites were extracted from each type of organs under study (leaves, roots and acorns), as described by (Valledor et al., 2014). 600 µL of cold (4oC) metabolite extraction buffer (methanol: chloroform: water; 5:2:2) were added to 15 mg of dried tissue (frozen, lyophilized weight). Powdered samples were extracted by vortexing for 10 s and sonicating in an ultrasonic bath at 4oC and maximum frequency (40 kHz). Samples were centrifuged at 20.000 g for 4 min at 4oC and the supernatant were transferred to 2 mL microcentrifuge tubes that contained 400 µL of phase separation mix (chloroform: water; 1:1). Tubes with metabolites were centrifuged at 20.000 g for 4 min at 4oC. The two phases were clearly defined with a sharp interface. Polar and non-polar metabolites, upper and lower layers respectively were transferred to new tubes. These two fractions were washed again (200 µL of cold (4oC) chloroform for polar layer and with 200 µL of cold (4oC) water for non-polar layer), centrifuged, and fractioned again. Polar and non-polar layers were saved to new tubes and dried completely with a micro concentrator Speedvac (Eppendorf Vacuum Concentrator Plus/5301).

Combined analysis:

Analysis ID AN001451
Analysis type MS
Chromatography type GC
Chromatography system Agilent
Column Agilent HP5-MS (30m × 0.25mm, 0.25 um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975B
Ion Mode POSITIVE
Units area

Chromatography:

Chromatography ID:CH001020
Instrument Name:Agilent
Column Name:Agilent HP5-MS (30m × 0.25mm, 0.25 um)
Chromatography Type:GC

MS:

MS ID:MS001341
Analysis ID:AN001451
Instrument Name:Agilent 5975B
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
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