Summary of Study ST001096

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 PR000733. The data can be accessed directly via it's Project DOI: 10.21228/M8XM40 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 IDST001096
Study TitleArabidopsis thaliana 25 accessions
Study SummaryWaters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
Institute
RIKEN
DepartmentCenter for Sustainable Resource Science
LaboratoryMetabolome Informatics Research Team
Last NameTsugawa
First NameHiroshi
Address1-7-22 Suehiro-cho, Tsurumi-ku
Emailhiroshi.tsugawa@riken.jp
Phone+81-45-503-9618
Submit Date2018-11-14
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Hiroshi Tsugawa Hiroshi Tsugawa
https://dx.doi.org/10.21228/M8XM40
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000733
Project DOI:doi: 10.21228/M8XM40
Project Title:Computational metabolomics to characterize metabolites in stable isotope-labelled organisms.
Project Summary:We developed a computational metabolomics workflow to characterize metabolite structures by using the set of fully 13C-labelled and non-labelled LC-MS/MS data. The platform was applied to structure elucidations for 31 tissues of 12 plant species, resulting in the assignments of 1,092 structures and 344 formulas to 3,604 carbon-determined metabolite ions. We also applied the methodology to find the trait-metabolite associations in natural accessions of Arabidopsis thaliana.
Institute:RIKEN
Department:Center for Sustainable Resource Science
Laboratory:Metabolome Informatics Research Team
Last Name:Tsugawa
First Name:Hiroshi
Address:1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
Email:hiroshi.tsugawa@riken.jp
Phone:+81-45-503-9618

Subject:

Subject ID:SU001140
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702
Genotype Strain:Col-0/Cvi-0/Bur-0/MIB-22/Shahdara/Fei-0/Bor-4/Ts-1/Tsu-0/RRS-7/Est-1/Ler-1/C24/RRS-10/Bla-1/Br-0/Got-7/Kas-2/Lov-5/Mr-0/Pna-17/T540/Tamm-2/UKNW06-460/Ty-0

Factors:

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

mb_sample_id local_sample_id ecotype tissue
SA074618R14_3Bla-1 root
SA074619R14_1Bla-1 root
SA074620R14_2Bla-1 root
SA074621S14_3Bla-1 shoot
SA074622S14_2Bla-1 shoot
SA074623S14_1Bla-1 shoot
SA074624R06_2Bor-4 root
SA074625R06_3Bor-4 root
SA074626R06_1Bor-4 root
SA074627S06_1Bor-4 shoot
SA074628S06_2Bor-4 shoot
SA074629S06_3Bor-4 shoot
SA074630R15_2Br-0 root
SA074631R15_3Br-0 root
SA074632R15_1Br-0 root
SA074633S15_1Br-0 shoot
SA074634S15_2Br-0 shoot
SA074635S15_3Br-0 shoot
SA074636R02_1Bur-0 root
SA074637R02_2Bur-0 root
SA074638R02_3Bur-0 root
SA074639S02_2Bur-0 shoot
SA074640S02_3Bur-0 shoot
SA074641S02_1Bur-0 shoot
SA074642R12_3C24 root
SA074643R12_2C24 root
SA074644R12_1C24 root
SA074645S12_1C24 shoot
SA074646S12_2C24 shoot
SA074647S12_3C24 shoot
SA074648R00_2Col-0 root
SA074649R00_3Col-0 root
SA074650R00_1Col-0 root
SA074651S00_1Col-0 shoot
SA074652S00_3Col-0 shoot
SA074653S00_2Col-0 shoot
SA074654R01_3Cvi-0 root
SA074655R01_1Cvi-0 root
SA074656R01_2Cvi-0 root
SA074657S01_3Cvi-0 shoot
SA074658S01_1Cvi-0 shoot
SA074659S01_2Cvi-0 shoot
SA074660R10_1Est-1 root
SA074661R10_3Est-1 root
SA074662R10_2Est-1 root
SA074663S10_1Est-1 shoot
SA074664S10_3Est-1 shoot
SA074665S10_2Est-1 shoot
SA074666R05_2Fei-0 root
SA074667R05_1Fei-0 root
SA074668R05_3Fei-0 root
SA074669S05_3Fei-0 shoot
SA074670S05_1Fei-0 shoot
SA074671S05_2Fei-0 shoot
SA074672R16_2Got-7 root
SA074673R16_3Got-7 root
SA074674R16_1Got-7 root
SA074675S16_1Got-7 shoot
SA074676S16_3Got-7 shoot
SA074677S16_2Got-7 shoot
SA074678R17_3Kas-2 root
SA074679R17_2Kas-2 root
SA074680R17_1Kas-2 root
SA074681S17_3Kas-2 shoot
SA074682S17_2Kas-2 shoot
SA074683S17_1Kas-2 shoot
SA074684R11_3Ler-1 root
SA074685R11_1Ler-1 root
SA074686R11_2Ler-1 root
SA074687S11_1Ler-1 shoot
SA074688S11_2Ler-1 shoot
SA074689S11_3Ler-1 shoot
SA074690R18_1Lov-5 root
SA074691R18_2Lov-5 root
SA074692R18_3Lov-5 root
SA074693S18_2Lov-5 shoot
SA074694S18_3Lov-5 shoot
SA074695S18_1Lov-5 shoot
SA074696R03_1MIB-22 root
SA074697R03_3MIB-22 root
SA074698R03_2MIB-22 root
SA074699S03_1MIB-22 shoot
SA074700S03_3MIB-22 shoot
SA074701S03_2MIB-22 shoot
SA074702R19_2Mr-0 root
SA074703R19_1Mr-0 root
SA074704R19_3Mr-0 root
SA074705S19_3Mr-0 shoot
SA074706S19_1Mr-0 shoot
SA074707S19_2Mr-0 shoot
SA074708R20_1Pna-17 root
SA074709R20_2Pna-17 root
SA074710R20_3Pna-17 root
SA074711S20_3Pna-17 shoot
SA074712S20_2Pna-17 shoot
SA074713S20_1Pna-17 shoot
SA074714R13_2RRS-10 root
SA074715R13_3RRS-10 root
SA074716R13_1RRS-10 root
SA074717S13_1RRS-10 shoot
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Collection:

Collection ID:CO001134
Collection Summary:The ABRC stock IDs are stored in the uploaded data folder. Sterilized seeds were kept for 2 days at 4 degreeC in the dark, and then sown on Murashige and Skoog (MS) medium agar containing 1% sucrose. All plates were placed in a growth chamber at 22 degreeC under a 16-hr light (approximately 40 micro mol/(sec m^2)/8-hr dark cycle. After 3-week cultivation the plants were harvested and shoot and root parts were immediately frozen in liquid nitrogen and lyophilized at -55 degreeC. Lyophilized samples were stored at -80 degreeC until use. Three technical replicates for each strain were prepared from quenched samples.
Sample Type:Plant

Treatment:

Treatment ID:TR001154
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001147
Sampleprep Summary:Samples (3 mg) of dried plant tissues were weighted in a 2.0-ml microtube (Sarstedt). Their metabolites were extracted with 150 µl of 80% MeOH containing 2.5 µM lidocaine and 10-camphour sulfonic acid per mg of dry weight using a mixer-mill with zirconia beads [7 min at 18 Hz and 4 degree C (MM300; Retsch)]. After 10-min centrifugation at 17,800 g the supernatant was filtered using an HLB µElution plate (Waters).

Combined analysis:

Analysis ID AN001783 AN001784
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2.1mm,1.7um) Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH001260
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:99.5% solvent A/0.5% solvent B at 0 min, 99.5%A/0.5%B at 0.1 min, 20%A/80%B at 10 min, 0.5%A/99.5%B at 10.1 min, 0.5%A/99.5%B at 12.0 min, 99.5%A/0.5%B at 12.1 min and 99.5%A/0.5%B at 15.0 min
Flow Rate:0.3 ml/min at 0 min, 0.3 ml/min at 10 min, 0.4 ml/min at 10.1 min, 0.4 ml/min at 14.4 min, and 0.3 ml/min at 14.5 min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001647
Analysis ID:AN001783
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:+3.00 kV
Collision Energy:6 V
Source Temperature:120
Desolvation Gas Flow:800 l/hr
Desolvation Temperature:450 degree C
Scan Range Moverz:50 - 1500
  
MS ID:MS001648
Analysis ID:AN001784
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:-2.75 kV
Collision Energy:6 V
Source Temperature:120
Desolvation Gas Flow:800 l/hr
Desolvation Temperature:450 degree C
Scan Range Moverz:50 - 1500
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