Summary of Study ST003861
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 PR002418. The data can be accessed directly via it's Project DOI: 10.21228/M83542 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 | ST003861 |
| Study Title | Comparative effects of nano urea and equimolar urea on the metabolome profile of Arabidopsis thaliana seedlings |
| Study Summary | We compared the effects of Indian Farmers Fertilizer Cooperative (IFFCO) nano urea formulation with equimolar conventional urea on the metabolome of Arabidopsis thaliana seedlings. Seedlings were grown in hydroponics in 1/4th strength Hoagland's solution for 12 days, then transferred to a nitrogen-free modified Hoagland's solution and grown for 21 days. Thereafter whole seedlings were crushed in lquid nitrogen to a fine powder. To 500 mg of fine powder, 5 mL of HPLC-grade methanol was added, and the sample was shaken/vortexed for over 30 minutes to extract analytes. The sample was spun at 8,000 rpm for 10 minutes to separate the liquid phase, which was then transferred to a fresh tube and stored at -20°C. Derivatization was not done, as it was not required for non-volatile compounds. Gas Chromatography-Mass Spectrometry was conducted using GC-MS model QP2010 (Shimadzu®) using a SH-I-5Sil MS Capillary (30 m x 0.25 mm x 0.25 µm) column. 2 µL of samples were injected using a splitless injection mode. Helium (1 mL/min) was used as a carrier gas. Ionization of 70 eV and a running time of 9.10 min – 52.0 min was used. The oven Program included an initial temperature of 45°C for 2 min, ramped to 140°C at 5°C/min, and then increased to 280°C, held isothermally for 10 min. The NIST14.L library (2020) was used to identify compounds based on retention times and mass spectra. |
| Institute | Indian Institute of Technology Jodhpur |
| Last Name | SADHUKHAN |
| First Name | AYAN |
| Address | NH62, NAGAUR ROAD |
| ayansadhukhan@iitj.ac.in | |
| Phone | 09038013015 |
| Submit Date | 2024-06-24 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf, qgd |
| Analysis Type Detail | GC-MS |
| Release Date | 2025-06-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002418 |
| Project DOI: | doi: 10.21228/M83542 |
| Project Title: | Comparative effects of nano urea and equimolar urea on the metabolome profile of Arabidopsis thaliana seedlings |
| Project Type: | GC MS |
| Project Summary: | We compared the effects of Indian Farmers Fertilizer Cooperative (IFFCO) nano urea formulation with equimolar conventional urea on the metabolome of Arabidopsis thaliana seedlings. Seedlings were grown in hydroponics in 1/4th strength Hoagland's solution for 12 days, then transferred to a nitrogen-free modified Hoagland's solution and grown for 21 days. Thereafter whole seedlings were crushed in lquid nitrogen to a fine powder. To 500 mg of fine powder, 5 mL of HPLC-grade methanol was added, and the sample was shaken/vortexed for over 30 minutes to extract analytes. The sample was spun at 8,000 rpm for 10 minutes to separate the liquid phase, which was then transferred to a fresh tube and stored at -20°C. Derivatization was not done, as it was not required for non-volatile compounds. Gas Chromatography-Mass Spectrometry was conducted using GC-MS model QP2010 (Shimadzu®) using a SH-I-5Sil MS Capillary (30 m x 0.25 mm x 0.25 µm) column. 2 µL of samples were injected using a splitless injection mode. Helium (1 mL/min) was used as a carrier gas. Ionization of 70 eV and a running time of 9.10 min – 52.0 min was used. The oven Program included an initial temperature of 45°C for 2 min, ramped to 140°C at 5°C/min, and then increased to 280°C, held isothermally for 10 min. The NIST14.L library (2020) was used to identify compounds based on retention times and mass spectra. |
| Institute: | Indian Institute of Technology Jodhpur |
| Department: | BIOSCIENCE AND BIOENGINEERING |
| Laboratory: | Plant functional genomics |
| Last Name: | SADHUKHAN |
| First Name: | AYAN |
| Address: | NH62, NAGAUR ROAD |
| Email: | ayansadhukhan@iitj.ac.in |
| Phone: | 09038013015 |
| Funding Source: | IFFCO |
Subject:
| Subject ID: | SU003995 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
Factors:
Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA424483 | 15d-c1-1 | Control |
| SA424484 | 15d-c2-2 | Control |
| SA424485 | 15d-c3-3 | Control |
| SA424486 | 15d-nu1-7 | nanourea |
| SA424487 | 15d-nu2-8 | nanourea |
| SA424488 | 15d-nu3-9 | nanourea |
| SA424489 | 15d-u1-4 | urea |
| SA424490 | 15d-u2-5 | urea |
| SA424491 | 15d-u3-6 | urea |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003988 |
| Collection Summary: | Seedlings were grown in hydroponics in 1/4th strength Hoagland's solution for 12 days, then transferred to a nitrogen-free modified Hoagland's solution and grown for 21 days. Thereafter whole seedlings were crushed in liquid nitrogen to a fine powder. |
| Sample Type: | Plant |
| Storage Conditions: | -80℃ |
| Collection Tube Temp: | -80C |
Treatment:
| Treatment ID: | TR004004 |
| Treatment Summary: | After 12 d hydroponic growth in nitrogen-containing media, then transferred to the nitrogen-free hydroponic media supplemented with 70 μM urea and nano urea, and were grown further for 21 days. On the 21st day, seedlings were harvested. |
Sample Preparation:
| Sampleprep ID: | SP004001 |
| Sampleprep Summary: | To 500 mg of fine powder of crushed seedlings, 5 mL of HPLC-grade methanol was added, and the sample was shaken/vortexed for over 30 minutes to extract analytes. The sample was centrifuged at 8,000 rpm for 10 minutes to separate the liquid phase, which was then transferred to a fresh tube and stored at -20°C. Note: Derivatization was not done, as it was not required for non-volatile compounds |
| Sample Derivatization: | Derivatization was not done, as it was not required for non-volatile compounds |
Chromatography:
| Chromatography ID: | CH004814 |
| Chromatography Summary: | Oven temperature was initially held at 45°C for 2 min then increased to 140°C at 5°C/min and finally increased to 280°C and held isothermally for 10 min. The sample injection was 2 μL and the carrier gas was helium at 1 mL/min. The ionization of the sample components was carried out 70 eV. The running time of the GC was from 9.10 min – 52.0 min. |
| Instrument Name: | Shimadzu GCMS-QP2010 ultra |
| Column Name: | Shimadzu SH-I-5Sil MS Capillary (30 m x 0.25 mm, 0.25um) |
| Column Temperature: | 45 °C for 2 min; then increased to 140 °C at 5°C/min; and finally increased to 280°C and held isothermally for 10 min |
| Flow Gradient: | - |
| Flow Rate: | 1 mL/min |
| Solvent A: | helium |
| Solvent B: | helium |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN006347 |
| Analysis Type: | MS |
| Chromatography ID: | CH004814 |
| Num Factors: | 3 |
| Num Metabolites: | 13 |
| Units: | intensity |
