Summary of Study ST001155
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 PR000774. The data can be accessed directly via it's Project DOI: 10.21228/M8N096 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 | ST001155 |
| Study Title | The Effect of Silicon on Salinity Tolerance and the Associated Metabolomics Profile Changes in Date Palm |
| Study Summary | Silicon has a promising role in the growth and salinity tolerance in plants. While the results obtained from the current study showed that silicon enhanced growth in date palm seedlings, the mechanism behind this observation was also investigated by studying changes occurred in metabolomic profiles triggered by silicon under salinity. The global metabolomic analysis using liquid-chromatography-mass-spectrometry revealed the presence of a number significantly (p ≤ 0.05) accumulated metabolites in leaves and roots when plants were irrigated with silicon and grown under control and salinity conditions. |
| Institute | Sultan Qaboos University |
| Department | Biology |
| Last Name | Yaish |
| First Name | Mahmoud |
| Address | Sultan Qaboos University, Department of Biology, College of Science |
| mack.yaish@gmail.com | |
| Phone | 968 24146823 |
| Submit Date | 2019-03-18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | metdb |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-03-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000774 |
| Project DOI: | doi: 10.21228/M8N096 |
| Project Title: | The Effect of Silicon on Salinity Tolerance and the Associated Metabolomics Profile Changes in Date Palm (Phoenix dactylifera L.) |
| Project Type: | Plant Metabolites |
| Project Summary: | Silicon has a promising role in the growth and salinity tolerance in plants. While the results obtained from the current study showed that silicon enhanced growth in date palm seedlings, the mechanism behind this observation was also investigated by studying changes occurred in metabolomic profiles triggered by silicon under salinity. The global metabolomic analysis using liquid-chromatography-mass-spectrometry revealed the presence of a number significantly (p ≤ 0.05) accumulated metabolites in leaves and roots when plants were irrigated with silicon and grown under control and salinity conditions. |
| Institute: | Sultan Qaboos University |
| Department: | Biology |
| Laboratory: | Mahmoud Yaish |
| Last Name: | Yaish |
| First Name: | Mahmoud |
| Address: | Department of Biology, College of Science, Sultan Qaboos University |
| Email: | mack.yaish@gmail.com |
| Phone: | 968 24146823 |
| Funding Source: | The research council of Oman, Oman |
Subject:
| Subject ID: | SU001220 |
| Subject Type: | Plant |
| Subject Species: | Phoenix dactylifera |
| Taxonomy ID: | 42345 |
Factors:
Subject type: Plant; Subject species: Phoenix dactylifera (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA080270 | CR3 | Contro-leaf |
| SA080271 | CR1 | Contro-leaf |
| SA080272 | CR2 | Contro-leaf |
| SA080273 | CL3 | Control-leaf |
| SA080274 | CL2 | Control-leaf |
| SA080275 | CL1 | Control-leaf |
| SA080276 | NL3 | NaCl-Leaf |
| SA080277 | NL2 | NaCl-Leaf |
| SA080278 | NL1 | NaCl-Leaf |
| SA080279 | NSiL3 | NaCl-Leaf-Si |
| SA080280 | NSiL1 | NaCl-Leaf-Si |
| SA080281 | NSiL2 | NaCl-Leaf-Si |
| SA080282 | NR1 | NaCl-Root |
| SA080283 | NR3 | NaCl-Root |
| SA080284 | NR2 | NaCl-Root |
| SA080285 | NSiR2 | NaCl-Root-Si |
| SA080286 | NSiR3 | NaCl-Root-Si |
| SA080287 | NSiR1 | NaCl-Root-Si |
| SA080288 | SiR2 | Siicon-root |
| SA080289 | SiR3 | Siicon-root |
| SA080290 | SiR1 | Siicon-root |
| SA080291 | SiL2 | silicon-leaf |
| SA080292 | SiL1 | silicon-leaf |
| SA080293 | SiL3 | silicon-leaf |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO001214 |
| Collection Summary: | Leaf and root tissues were collected from date palm seedlings after treatment with NaCl and/or silicon, flash frozen with liquid nitrogen, and freeze dried. |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR001235 |
| Treatment Summary: | Once the radicle of the seeds had emerged, they were then transferred to potting compost and maintained at 32C/30C with a photoperiod of 16/8 h in the growth chamber. The seedlings were then divided into four sets based on their treatments and were irrigated either with tap water with an electrical conductivity of 50 mS/m, considered as a control treatment (control), 300 mM NaCl without additional silicon for salt stress (NaCl), 5 mM Na2SiO3 (+Si) for silicon treatment or 5 mM of sodium silicate (Na2SiO3) along with 300 mM NaCl (NaCl+Si) for salt stress and silicon treatment. The NaCl and silicon treatments were administered on a weekly basis, as irrigation. |
Sample Preparation:
| Sampleprep ID: | SP001228 |
| Sampleprep Summary: | A total of 24 samples were analyzed using LC-MS by HILIC chromatography on a 0.5 x 150 mm Zic-pHILIC column using 10 mM NH4HCO3 in water (A) and 10 mM NH4HCO3 in 95% acetonitrile (B) as solvents and by RPLC chromatography using the same solvents and a 0.5 x 100 mm PLRPS column. The Samples were extracted at a tissue concentration of 100 mg/mL (leaves) or 50 mg/mL (roots) in 80% methanol by vortexing for 10 minutes. The solids were collected by centrifugation, and then the supernatant was filtered through a 0.8 μm spin filter. Samples were injected onto the LC-MS and data was acquired in polarity switching mode with data dependent acquisition of MS/MS spectra. |
Combined analysis:
| Analysis ID | AN001911 | AN001912 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Q-Exactive | Thermo Q-Exactive |
| Column | Zic-pHILIC 0.5 x 150 mm | 0.5 x 100 mm PLRPS column |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED | UNSPECIFIED |
| Units | log10(peak area) | log10(peak area) |
Chromatography:
| Chromatography ID: | CH001384 |
| Instrument Name: | Thermo Q-Exactive |
| Column Name: | Zic-pHILIC 0.5 x 150 mm |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001385 |
| Instrument Name: | Thermo Q-Exactive |
| Column Name: | 0.5 x 100 mm PLRPS column |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001767 |
| Analysis ID: | AN001911 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were injected onto the LC-MS and data was acquired in polarity switching mode with data dependent acquisition of MS/MS spectra. The ion mode is polarity-switching, which means it scans in positive and negative ion mode during the sample run, switching between the two modes about every 20 milliseconds. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS001768 |
| Analysis ID: | AN001912 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were injected onto the LC-MS and data was acquired in polarity switching mode with data dependent acquisition of MS/MS spectra. The ion mode is polarity-switching, which means it scans in positive and negative ion mode during the sample run, switching between the two modes about every 20 milliseconds. |
| Ion Mode: | UNSPECIFIED |
