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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
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

Select appropriate tab below to view additional metadata details:

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
Species Group:Plants

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
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 150

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
Chromatography ID CH001260 CH001260
MS ID MS001647 MS001648
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
  logo