Summary of Study ST000320
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 PR000259. The data can be accessed directly via it's Project DOI: 10.21228/M89K5F This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000320 |
| Study Title | Single treatment gene impact on Arabidopsis metabolites |
| Study Summary | This experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2014-12-22 |
| Num Groups | 6 |
| Total Subjects | 34 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-01-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000259 |
| Project DOI: | doi: 10.21228/M89K5F |
| Project Title: | Single treatment gene impact on Arabidopsis metabolites |
| Project Summary: | This experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | U24DK097154 |
Subject:
| Subject ID: | SU000340 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
| Species Group: | Plant |
Factors:
Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA014497 | Seed-111-1B | 111 |
| SA014498 | Seed-111-2B | 111 |
| SA014499 | Seed-111-3B | 111 |
| SA014500 | Seed-111-1A | 111 |
| SA014501 | Seed-111-3A | 111 |
| SA014502 | Seed-111-2A | 111 |
| SA014503 | Seed-133-2A | 133 |
| SA014504 | Seed-133-2B | 133 |
| SA014505 | Seed-133-3A | 133 |
| SA014506 | Seed-133-1B | 133 |
| SA014507 | Seed-133-1A | 133 |
| SA014508 | Seed-Control-A | Control |
| SA014509 | Seed-Control-B | Control |
| SA014510 | Seed-Control-E | Control |
| SA014511 | Seed-Control-D | Control |
| SA014512 | Seed-Control-C | Control |
| SA014513 | Seed-Control-F | Control |
| Showing results 1 to 17 of 17 |
Collection:
| Collection ID: | CO000334 |
| Collection Summary: | Plants are 30-35d old. They were harvested in liquid N2, grounded to fine powder, distributed to individual falcon tubes and kept at dry ice before handing over the sample to core facility. |
| Collection Protocol Filename: | StudyDesign-AvinashSrivastava-82514.pdf |
| Sample Type: | Seeds |
Treatment:
| Treatment ID: | TR000354 |
| Treatment Summary: | Single treatment gene impact on plant metabolites and compared to WT control: 1. Control (A,B,C,D,E,F total 6 replicates) 2. Sample 1 (A,B,C,D,E,F total 6 replicates) 3. Sample 2. (A,B,C,D,E,F total 6 replicates) |
| Treatment Protocol Filename: | StudyDesign-AvinashSrivastava-82514.pdf |
Sample Preparation:
| Sampleprep ID: | SP000348 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | Sample_Prep_Avinash_Srivastava_mx_188894.pdf |
Combined analysis:
| Analysis ID | AN000508 | AN000509 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Unspecified | Unspecified |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
Chromatography:
| Chromatography ID: | CH000358 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Unspecified |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000444 |
| Analysis ID: | AN000508 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000445 |
| Analysis ID: | AN000509 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
