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.

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Study IDST000289
Study TitlePPDK RNAi effects in endosperm metabolite pools
Study SummaryMaize 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
DepartmentSECIM
LaboratoryStewart
Last NameStewart
First NameJon
Address102 Leigh Hall
Emailjds2@chem.ufl.edu
Phone352-846-0743
Submit Date2015-08-17
Num Groups2
Total Subjects6
Raw Data AvailableYes
Raw Data File Type(s).mzML
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version1
Jon Stewart Jon Stewart
https://dx.doi.org/10.21228/M8SP4F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA013158Stewart_WT_tube_1515_1control
SA013159Stewart_WT_tube_1515_2control
SA013160Stewart_WT_tube_604_2control
SA013161Stewart_WT_tube_1019_2control
SA013162Stewart_WT_tube_604_1control
SA013163Stewart_WT_tube_1019_1control
SA013164Stewart_27kDPDKRNAi_#1_tube_604_1mutant
SA013165Stewart_27kDPDKRNAi_#1_tube_1019_2mutant
SA013166Stewart_27kDPDKRNAi_#1_tube_604_2mutant
SA013167Stewart_27kDPDKRNAi_#33_tube_1515_1mutant
SA013168Stewart_27kDPDKRNAi_#33_tube_1515_2mutant
SA013169Stewart_27kDPDKRNAi_#1_tube_1019_1mutant
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)
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
  
MS ID:MS000401
Analysis ID:AN000461
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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