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
| 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 |
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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 |
Combined analysis:
| Analysis ID | AN006347 |
|---|---|
| Chromatography ID | CH004814 |
| MS ID | MS006048 |
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Shimadzu GCMS-QP2010 ultra |
| Column | Shimadzu SH-I-5Sil MS Capillary (30 m x 0.25 mm, 0.25um) |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Shimadzu QP2010 Ultra |
| Ion Mode | POSITIVE |
| Units | intensity |
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 |
MS:
| MS ID: | MS006048 |
| Analysis ID: | AN006347 |
| Instrument Name: | Shimadzu QP2010 Ultra |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | NIST14.L library (2020) was then searched to compare the structures of the compounds with that of the NIST database. Compounds were then identified based on the retention times and mass spectra with already known compounds in the NIST library (NIST14.L). |
| Ion Mode: | POSITIVE |
