Summary of Study ST000289
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 PR000231. The data can be accessed directly via it's Project DOI: 10.21228/M8SP4F 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 | ST000289 |
| Study Title | PPDK RNAi effects in endosperm metabolite pools |
| Study Summary | Maize plants were transformed with endosperm-specific PPDK RNAi knockout constructs to alter starch/protein ratios. Metabolite pool comparisons will be examined from sibling kernels harvested from segregating ears. |
| Institute | University of Florida |
| Department | SECIM |
| Laboratory | Stewart |
| Last Name | Stewart |
| First Name | Jon |
| Address | 102 Leigh Hall |
| jds2@chem.ufl.edu | |
| Phone | 352-846-0743 |
| Submit Date | 2015-08-17 |
| Num Groups | 2 |
| Total Subjects | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000231 |
| Project DOI: | doi: 10.21228/M8SP4F |
| Project Title: | Climate Change and Starch Yield in Maize Part 1 |
| Project Type: | MS study |
| Project Summary: | Comparison of unaltered inbred maize endosperm metabolite pools with corresponding tissues from the same time in development but from plants lacking both PDK1 and PDK2 |
| Institute: | Iowa State University |
| Department: | Biochemistry, Biophysics, and Mol. Biol. |
| Laboratory: | Myers/Hennen-Bierwagen |
| Last Name: | Hennen-Bierwagen |
| First Name: | Tracie |
| Address: | 2154 Mol. Biol. Blg, ISU, Ames, IA |
| Email: | tabier@iastate.edu |
| Phone: | 515-294-9548 |
| Funding Source: | USDA |
Subject:
| Subject ID: | SU000309 |
| Subject Type: | Plant |
| Subject Species: | Zea mays |
| Taxonomy ID: | 4577 |
| Species Group: | Plant |
Factors:
Subject type: Plant; Subject species: Zea mays (Factor headings shown in green)
| mb_sample_id | local_sample_id | Tissue |
|---|---|---|
| SA013158 | Stewart_WT_tube_1515_1 | control |
| SA013159 | Stewart_WT_tube_1515_2 | control |
| SA013160 | Stewart_WT_tube_604_2 | control |
| SA013161 | Stewart_WT_tube_1019_2 | control |
| SA013162 | Stewart_WT_tube_604_1 | control |
| SA013163 | Stewart_WT_tube_1019_1 | control |
| SA013164 | Stewart_27kDPDKRNAi_#1_tube_604_1 | mutant |
| SA013165 | Stewart_27kDPDKRNAi_#1_tube_1019_2 | mutant |
| SA013166 | Stewart_27kDPDKRNAi_#1_tube_604_2 | mutant |
| SA013167 | Stewart_27kDPDKRNAi_#33_tube_1515_1 | mutant |
| SA013168 | Stewart_27kDPDKRNAi_#33_tube_1515_2 | mutant |
| SA013169 | Stewart_27kDPDKRNAi_#1_tube_1019_1 | mutant |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000303 |
| Collection Summary: | n/a |
| Sample Type: | maize starchy endosperm |
| Collection Method: | manual removal from maize ear |
| Collection Location: | Iowa State University |
| Storage Conditions: | ear frozen in liquid N2, kernels removed while frozen, and maintained at -80C |
Treatment:
| Treatment ID: | TR000323 |
| Treatment Summary: | Each ear is segregating both mutant and wild type kernels, thus the harvest and freezing for the controls is the exact same as the mutant sibling kernels from the same ear. |
| Plant Growth Location: | Woodruff Farm, Story Co., Ames, IA |
| Plant Plot Design: | 10 plants/row; random row placement over 0.5 acres |
| Plant Light Period: | natural sunlight and day length, summer 2014 |
| Plant Estab Date: | 2014-05-01 |
| Plant Growth Stage: | 20 days after pollination |
| Plant Metab Quench Method: | flash frozen in liquid N2, maintained at -80C |
Sample Preparation:
| Sampleprep ID: | SP000317 |
| Sampleprep Summary: | n/a |
| Sampleprep Protocol Filename: | Plant_Tissue.pdf |
Combined analysis:
| Analysis ID | AN000460 | AN000461 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Scientific-Dionex Ultimate 3000 | Thermo Scientific-Dionex Ultimate 3000 |
| Column | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000328 |
| Methods Filename: | Instrument_Parameters.pdf |
| Instrument Name: | Thermo Scientific-Dionex Ultimate 3000 |
| Column Name: | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) |
| Flow Rate: | 350 ul/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000400 |
| Analysis ID: | AN000460 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Instrument_Parameters.pdf |
| MS ID: | MS000401 |
| Analysis ID: | AN000461 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Instrument_Parameters.pdf |
