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.
| Study ID | ST000889 |
| Study Title | GC-MS analysis of Quercus ilex organs (leaves, roots and acorns) |
| Study Type | Untargeted metabolomics |
| Study Summary | Qualitative metabolomics study on leaves, roots and acorns from Quercus ilex plantlets. We analyzed polar(metanol:water) and apolar (chloroform) fractions. |
| 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 |
| n12lohic@uco.es | |
| Phone | 626894948 |
| Submit Date | 2017-10-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2018-06-05 |
| Release Version | 1 |
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 |
|---|---|---|
| SA052409 | Acorn1 | Acorn |
| SA052410 | Acorn3 | Acorn |
| SA052411 | Acorn2 | Acorn |
| SA052412 | Leaf3 | Leaf |
| SA052413 | Leaf2 | Leaf |
| SA052414 | Leaf1 | Leaf |
| SA052415 | Root3 | Root |
| SA052416 | Root2 | Root |
| SA052417 | Root1 | Root |
| 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 |
