Summary of study ST000013

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 PR000012. The data can be accessed directly via it's Project DOI: 10.21228/M8KW2W This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000013
Study TitleMutation Study
Study TypeGenotype
Study SummaryThis experiment tests the effect of individual mutations on the metabolome of Arabidopsis. The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate. 2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose. 3. Prior to sowing, seeds were sterilized by treating for 1-minute at room temperature with a 300-l solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water. 4. Upon sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, catalogue #1530-0), and then stored horizontally for 4-days at 4 °C, with illumination of 1 mol/m2. 5. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexi-glass holders for 17-days this growth room condition is labeled in Table I. 6. On 18th day Petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening. 7. Upon harvesting, plant material was quenched by immersion in liquid nitrogen and stored at 70 °C.
Institute
University of California, Davis
DepartmentDavis Genome Center
LaboratoryFiehn
Last NameKind
First NameTobias
Address451 E. Health Sci. Drive, Davis, California 95616, USA
Emailtkind@ucdavis.edu
Submit Date2013-05-20
Num Groups15
Total Subjects90
Raw Data AvailableNo
Analysis Type DetailGC-MS
Release Date2013-06-19
Release Version1
Tobias Kind Tobias Kind
https://dx.doi.org/10.21228/M8KW2W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000012
Project DOI:doi: 10.21228/M8KW2W
Project Title:Seeds Mutant Experiment
Project Type:Genotype
Project Summary:The effect of individual mutations on the metabolome of Arabidopsis
Institute:University of California, Davis
Department:Davis Genome Center
Laboratory:Fiehn
Last Name:Fiehn
First Name:Oliver
Address:451 E. Health Sci. Drive, Davis, California 95616, USA
Email:ofiehn@ucdavis.edu

Subject:

Subject ID:SU000015
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702
Genotype Strain:Wild type Col0: 1 | Wild type Col0: 2 | SAIL_6_G_02 | SALK_024747 | SALK_135268 | SALK_077749 | SALK_114456 | SALK_021832 | SALK_125505 | SALK_022584 | SALK_062847 | SALK_148208 | SALK_016312 | CS24090 | SALK_083600
Species Group:Plant

Factors:

Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id local_sample_id genotype
SA000720343938CS24090
SA000721343942CS24090
SA000722343946CS24090
SA000723343950CS24090
SA000724343954CS24090
SA000725343958CS24090
SA000654343655SAIL_6_G_02
SA000655343659SAIL_6_G_02
SA000656343663SAIL_6_G_02
SA000657343667SAIL_6_G_02
SA000658343671SAIL_6_G_02
SA000659343675SAIL_6_G_02
SA000714343913SALK_016312
SA000715343917SALK_016312
SA000716343921SALK_016312
SA000717343925SALK_016312
SA000718343929SALK_016312
SA000719343933SALK_016312
SA000684343780SALK_021832
SA000685343784SALK_021832
SA000686343788SALK_021832
SA000687343792SALK_021832
SA000688343796SALK_021832
SA000689343800SALK_021832
SA000696343830SALK_022584
SA000697343834SALK_022584
SA000698343838SALK_022584
SA000699343842SALK_022584
SA000700343846SALK_022584
SA000701343850SALK_022584
SA000660343680SALK_024747
SA000661343684SALK_024747
SA000662343688SALK_024747
SA000663343692SALK_024747
SA000664343696SALK_024747
SA000665343700SALK_024747
SA000702343855SALK_062847
SA000703343859SALK_062847
SA000704343863SALK_062847
SA000705343867SALK_062847
SA000706343871SALK_062847
SA000707343875SALK_062847
SA000672343730SALK_077749
SA000673343734SALK_077749
SA000674343738SALK_077749
SA000675343742SALK_077749
SA000676343746SALK_077749
SA000677343750SALK_077749
SA000726343963SALK_083600
SA000727343967SALK_083600
SA000728343971SALK_083600
SA000729343975SALK_083600
SA000730343979SALK_083600
SA000731343983SALK_083600
SA000678343755SALK_114456
SA000679343759SALK_114456
SA000680343763SALK_114456
SA000681343767SALK_114456
SA000682343771SALK_114456
SA000683343775SALK_114456
SA000690343805SALK_125505
SA000691343809SALK_125505
SA000692343813SALK_125505
SA000693343817SALK_125505
SA000694343821SALK_125505
SA000695343825SALK_125505
SA000666343705SALK_135268
SA000667343709SALK_135268
SA000668343713SALK_135268
SA000669343717SALK_135268
SA000670343721SALK_135268
SA000671343725SALK_135268
SA000708343888SALK_148208
SA000709343892SALK_148208
SA000710343896SALK_148208
SA000711343900SALK_148208
SA000712343904SALK_148208
SA000713343908SALK_148208
SA000642343605Wild type Col0: 1
SA000643343609Wild type Col0: 1
SA000644343613Wild type Col0: 1
SA000645343617Wild type Col0: 1
SA000646343621Wild type Col0: 1
SA000647343625Wild type Col0: 1
SA000648343630Wild type Col0: 2
SA000649343634Wild type Col0: 2
SA000650343638Wild type Col0: 2
SA000651343642Wild type Col0: 2
SA000652343646Wild type Col0: 2
SA000653343650Wild type Col0: 2
Showing results 1 to 90 of 90

Collection:

Collection ID:CO000013
Sample Type:Plant

Treatment:

Treatment ID:TR000021
Plant Growth Support:Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose. Prior to sowing, seeds were sterilized by treating for 1-minute at room temperature with a 300-l solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water. Upon sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, catalogue #1530-0), and then stored horizontally for 4-days at 4°C, with illumination of 1 mol/m2. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexi-glass holders for 17-days. This growth room condition is labeled in Table I. On 18th day Petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening. Upon harvesting, plant material was quenched by immersion in liquid nitrogen and stored at 70°C.
Plant Plot Design:Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.
Plant Light Period:24h a day at 80 fluence
Plant Humidity:Day 100%, Night 100%
Plant Temp:Day 24 C, Night 24 C
Plant Nutritional Regime:Each plate contains between 20 and 25-ml of sterile MS media: 0.1% sucrose, 1x MS vitamins, 4.3 g MS salt pH 5.7 with 15 g/L Bacto agar
Plant Metab Quench Method:immersion in liquid nitrogen and stored at 70C
Plant Harvest Method:On 18th day Petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening

Sample Preparation:

Sampleprep ID:SP000026

Combined analysis:

Analysis ID AN000030
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units Peak height

Chromatography:

Chromatography ID:CH000013
Chromatography Comments:Gas Chromatograph (GC) Methods quick-splitless_working
Instrument Name:Agilent 6890N
Chromatography Type:GC

MS:

MS ID:MS000029
Analysis ID:AN000030
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Mass Spectrometer (MS) Methods quick_1700V
Ion Mode:POSITIVE
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