Summary of Study ST002201

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 PR001404. The data can be accessed directly via it's Project DOI: 10.21228/M87M6J This work is supported by NIH grant, U2C- DK119886.

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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 IDST002201
Study TitleMulti-omics profiling of 5 Arabidopsis accessions in response to combined water and nitrogen deficiencies.
Study TypeMulti-omics analysis
Study SummaryIn this study, we build an in-depth multi-omics profile of 5 Arabidopsis accessions, in order to find the inner relations of N deficit, mild drought, and combined stress response at different scales. We used our own phenotyping platform (Phenoscope) to handle hundreds of Arabidopsis plants across 20 modalities (5 Genotypes x 2 Treatments of Water availability x 2 Treatments of Nitrogen availablity), phenotype those plants for growth-related traits and ultimately harvest the samples used in transcriptomics, metabolomics and physiological profiling. Then we have analysed those data to reveal in particular the specificities of the response to stress in each accession, as well as the W x N interactions leading to patterns that are specific to the combined stress response. The metabolomics data is particularly useful to highlight for instance the very specific profile of the Cvi-0 accession overall, or the larger extent of the metabolite responsiveness to N-deficiency with respect to mild drought. The share of the stress response that is specific to the combined stress condition is also quite variable between the 5 accessions.
Institute
INRAE
DepartmentInstitut Jean-Pierre Bourgin, IJPB UMR1318 INRAE-AgroParisTech
LaboratoryPlateforme de Chimie
Last NameCLEMENT
First NameGilles
AddressEtoile de Choisy (route de St Cyr) 78026 Versailles Cedex
Emailgilles.clement@inrae.fr
Phone+33 (0) 1 30 83 31 67
Submit Date2022-06-16
Num Groups20
Total Subjects163
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2024-06-06
Release Version1
Gilles CLEMENT Gilles CLEMENT
https://dx.doi.org/10.21228/M87M6J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001404
Project DOI:doi: 10.21228/M87M6J
Project Title:Variation and Abiotic Stress Tolerance
Project Type:Quantitative genetics of plant interaction with their environment
Project Summary:Study of the genetic architecture of complex traits: what is the genetic (or epigenetic) basis for variation in size, form, environmental responses... that shape the green world. In other words, what is the genotype to phenotype equation These questions are studied taking advantage of the natural diversity existing within a wild and model species (Arabidopsis thaliana), combined to novel high-throughput phenotyping robots, with the help of Mathematics.
Institute:INRAE
Department:Institut Jean-Pierre Bourgin, IJPB UMR1318 INRAE-AgroParisTech
Laboratory:Variation and Abiotic Stress Tolerance
Last Name:LOUDET
First Name:Olivier
Address:Route de ST-Cyr, Versailles, Ile de France, 78026, France
Email:Olivier.Loudet@inrae.fr
Phone:+33 (0) 1 30 83 32 17

Subject:

Subject ID:SU002287
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702

Factors:

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

mb_sample_id local_sample_id Genotype Drought Nitrogen
SA211180Bur-0_W-N-_P3ID33_dBur-0 W- N-
SA211181Bur-0_W-N-_P3ID34_cBur-0 W- N-
SA211182Bur-0_W-N-_P3ID33_cBur-0 W- N-
SA211183Bur-0_W-N-_P3ID33_bBur-0 W- N-
SA211184Bur-0_W-N-_P3ID33_fBur-0 W- N-
SA211185Bur-0_W-N-_P3ID33_aBur-0 W- N-
SA211186Bur-0_W-N-_P3ID33_eBur-0 W- N-
SA211187Bur-0_W-N-_P3ID34_dBur-0 W- N-
SA211188Bur-0_W-N-_P3ID34_aBur-0 W- N-
SA211189Bur-0_W-N-_P3ID34_eBur-0 W- N-
SA211190Bur-0_W-N-_P3ID34_bBur-0 W- N-
SA211172Bur-0_W-N+_P3ID34_aBur-0 W- N+
SA211173Bur-0_W-N+_P3ID33_dBur-0 W- N+
SA211174Bur-0_W-N+_P3ID34_cBur-0 W- N+
SA211175Bur-0_W-N+_P3ID34_dBur-0 W- N+
SA211176Bur-0_W-N+_P3ID34_bBur-0 W- N+
SA211177Bur-0_W-N+_P3ID33_cBur-0 W- N+
SA211178Bur-0_W-N+_P3ID33_bBur-0 W- N+
SA211179Bur-0_W-N+_P3ID33_aBur-0 W- N+
SA211164Bur-0_W+N-_P3ID33_dBur-0 W+ N-
SA211165Bur-0_W+N-_P3ID34_aBur-0 W+ N-
SA211166Bur-0_W+N-_P3ID34_bBur-0 W+ N-
SA211167Bur-0_W+N-_P3ID34_cBur-0 W+ N-
SA211168Bur-0_W+N-_P3ID33_cBur-0 W+ N-
SA211169Bur-0_W+N-_P3ID34_dBur-0 W+ N-
SA211170Bur-0_W+N-_P3ID33_bBur-0 W+ N-
SA211171Bur-0_W+N-_P3ID33_aBur-0 W+ N-
SA211157Bur-0_W+N+_P3ID33_dBur-0 W+ N+
SA211158Bur-0_W+N+_P3ID33_cBur-0 W+ N+
SA211159Bur-0_W+N+_P3ID34_aBur-0 W+ N+
SA211160Bur-0_W+N+_P3ID34_cBur-0 W+ N+
SA211161Bur-0_W+N+_P3ID34_dBur-0 W+ N+
SA211162Bur-0_W+N+_P3ID33_bBur-0 W+ N+
SA211163Bur-0_W+N+_P3ID33_aBur-0 W+ N+
SA211212Col-0_W-N-_P3ID33_fCol-0 W- N-
SA211213Col-0_W-N-_P3ID33_dCol-0 W- N-
SA211214Col-0_W-N-_P3ID33_cCol-0 W- N-
SA211215Col-0_W-N-_P3ID33_bCol-0 W- N-
SA211216Col-0_W-N-_P3ID34_eCol-0 W- N-
SA211217Col-0_W-N-_P3ID33_aCol-0 W- N-
SA211218Col-0_W-N-_P3ID33_eCol-0 W- N-
SA211219Col-0_W-N-_P3ID34_dCol-0 W- N-
SA211220Col-0_W-N-_P3ID34_bCol-0 W- N-
SA211221Col-0_W-N-_P3ID34_cCol-0 W- N-
SA211222Col-0_W-N-_P3ID34_aCol-0 W- N-
SA211205Col-0_W-N+_P3ID33_dCol-0 W- N+
SA211206Col-0_W-N+_P3ID34_aCol-0 W- N+
SA211207Col-0_W-N+_P3ID33_cCol-0 W- N+
SA211208Col-0_W-N+_P3ID33_aCol-0 W- N+
SA211209Col-0_W-N+_P3ID34_dCol-0 W- N+
SA211210Col-0_W-N+_P3ID34_bCol-0 W- N+
SA211211Col-0_W-N+_P3ID33_bCol-0 W- N+
SA211199Col-0_W+N-_P3ID34_aCol-0 W+ N-
SA211200Col-0_W+N-_P3ID34_cCol-0 W+ N-
SA211201Col-0_W+N-_P3ID34_bCol-0 W+ N-
SA211202Col-0_W+N-_P3ID33_cCol-0 W+ N-
SA211203Col-0_W+N-_P3ID33_bCol-0 W+ N-
SA211204Col-0_W+N-_P3ID33_aCol-0 W+ N-
SA211191Col-0_W+N+_P3ID33_dCol-0 W+ N+
SA211192Col-0_W+N+_P3ID33_cCol-0 W+ N+
SA211193Col-0_W+N+_P3ID33_bCol-0 W+ N+
SA211194Col-0_W+N+_P3ID34_aCol-0 W+ N+
SA211195Col-0_W+N+_P3ID33_aCol-0 W+ N+
SA211196Col-0_W+N+_P3ID34_bCol-0 W+ N+
SA211197Col-0_W+N+_P3ID34_dCol-0 W+ N+
SA211198Col-0_W+N+_P3ID34_cCol-0 W+ N+
SA211246Cvi-0_W-N-_P3ID33_eCvi-0 W- N-
SA211247Cvi-0_W-N-_P3ID33_dCvi-0 W- N-
SA211248Cvi-0_W-N-_P3ID33_aCvi-0 W- N-
SA211249Cvi-0_W-N-_P3ID33_fCvi-0 W- N-
SA211250Cvi-0_W-N-_P3ID33_bCvi-0 W- N-
SA211251Cvi-0_W-N-_P3ID33_cCvi-0 W- N-
SA211252Cvi-0_W-N-_P3ID34_aCvi-0 W- N-
SA211253Cvi-0_W-N-_P3ID34_dCvi-0 W- N-
SA211254Cvi-0_W-N-_P3ID34_cCvi-0 W- N-
SA211255Cvi-0_W-N-_P3ID34_bCvi-0 W- N-
SA211256Cvi-0_W-N-_P3ID34_eCvi-0 W- N-
SA211238Cvi-0_W-N+_P3ID34_bCvi-0 W- N+
SA211239Cvi-0_W-N+_P3ID34_cCvi-0 W- N+
SA211240Cvi-0_W-N+_P3ID34_dCvi-0 W- N+
SA211241Cvi-0_W-N+_P3ID34_aCvi-0 W- N+
SA211242Cvi-0_W-N+_P3ID33_dCvi-0 W- N+
SA211243Cvi-0_W-N+_P3ID33_bCvi-0 W- N+
SA211244Cvi-0_W-N+_P3ID33_aCvi-0 W- N+
SA211245Cvi-0_W-N+_P3ID33_cCvi-0 W- N+
SA211231Cvi-0_W+N-_P3ID34_aCvi-0 W+ N-
SA211232Cvi-0_W+N-_P3ID33_cCvi-0 W+ N-
SA211233Cvi-0_W+N-_P3ID34_dCvi-0 W+ N-
SA211234Cvi-0_W+N-_P3ID34_cCvi-0 W+ N-
SA211235Cvi-0_W+N-_P3ID34_bCvi-0 W+ N-
SA211236Cvi-0_W+N-_P3ID33_aCvi-0 W+ N-
SA211237Cvi-0_W+N-_P3ID33_bCvi-0 W+ N-
SA211223Cvi-0_W+N+_P3ID33_cCvi-0 W+ N+
SA211224Cvi-0_W+N+_P3ID33_bCvi-0 W+ N+
SA211225Cvi-0_W+N+_P3ID33_aCvi-0 W+ N+
SA211226Cvi-0_W+N+_P3ID33_dCvi-0 W+ N+
SA211227Cvi-0_W+N+_P3ID34_dCvi-0 W+ N+
SA211228Cvi-0_W+N+_P3ID34_aCvi-0 W+ N+
SA211229Cvi-0_W+N+_P3ID34_cCvi-0 W+ N+
SA211230Cvi-0_W+N+_P3ID34_bCvi-0 W+ N+
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Collection:

Collection ID:CO002280
Collection Summary:Arabidopsis shoots were harvested and inserted in a previously weighed eppendorf tubes, frozen in liquid nitrogen and weighed fastly again. They were grinded by shaking with a metal ball.
Sample Type:Plant
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002299
Treatment Summary:We applied a combination of soil water content (SWC; adjusted with respect to complete soil saturation) and nutrient solution (adjusted to provide a specific amount of nitrate over the course of the experiment : 160.45 ± 7.96 ml of 5mM [Nitrate] nutrient solution in total for the control condition W+N+; 50.85 ± 4.67 ml of 5mM [Nitrate] in total for the single drought stress condition W-N+; 161.93 ± 11.07 ml of 0.5mM [Nitrate] in total for the single N-deficiency condition W+N-; 50.70 ± 4.10 ml of 1.5mM [Nitrate] in total for the combined stress condition W-N-) to establish the different conditions

Sample Preparation:

Sampleprep ID:SP002293
Sampleprep Summary:All steps were performed in 2 ml Safelock Eppendorf tubes. The ground frozen samples (25 mg) were resuspended in 1 ml of frozen (-20°C) Water:Acetonitrile:Isopropanol (2:3:3) containing Ribitol at 4 µg/ml and extracted for 10 min at 4°C with shaking at 1400 rpm in an Eppendorf Thermomixer. Insoluble material was removed by centrifugation at 20000g for 5 min. 66 µl were collected and dried overnight at 35 °C in a Speed-Vac . Fiehn et al (the Plant Journal (2008) 53, 691-704).
Processing Storage Conditions:-20℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003604
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Restek Rxi-5Sil (30m x 0.25mm,0.25m) with 10m precolumn
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5977B
Ion Mode POSITIVE
Units µg/mg FW and arbitrary/mg FW

Chromatography:

Chromatography ID:CH002664
Chromatography Summary:The instrument was an Agilent 7890B gas chromatograph coupled to an Agilent 5977B mass spectrometer. The column was an Rxi-5SilMS from Restek (30 m with 10 m integraguard column). The liner (Restek # 20994) was changed before the analysis. Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 330 °C for 5 min (run length 38 min). Helium constant flow was 0.7 mL/min. Temperatures were the following: injector: 250°C, transfer line: 290°C, source: 250 °C and quadripole 150 °C. 5 scans per second were acquired spanning a 50 to 600 Da range. Instrument was tuned with PFTBA with the 69 m/z and 219 m/z of equal intensities. 5 scans per second were acquired. The split mode conditions were: 70°C for 2 min then 30°C per min to 330 °C for 5 min. Helium constant flow 1 mL/min.
Instrument Name:Agilent 7890B
Column Name:Restek Rxi-5Sil (30m x 0.25mm,0.25m) with 10m precolumn
Chromatography Type:GC

MS:

MS ID:MS003359
Analysis ID:AN003604
Instrument Name:Agilent 5977B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:The instrument was an Agilent 7890B gas chromatograph coupled to an Agilent 5977B mass spectrometer. The column was an Rxi-5SilMS from Restek (30 m with 10 m integraguard column). The liner (Restek # 20994) was changed before the analysis. Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 330 °C for 5 min (run length 38 min). Helium constant flow was 0.7 mL/min. Temperatures were the following: injector: 250°C, transfer line: 290°C, source: 250 °C and quadripole 150 °C. 5 scans per second were acquired spanning a 50 to 600 Da range. Instrument was tuned with PFTBA with the 69 m/z and 219 m/z of equal intensities. 5 scans per second were acquired. The split mode conditions were: 70°C for 2 min then 30°C per min to 330 °C for 5 min. Helium constant flow 1 mL/min.Data processing: Raw Agilent datafiles were converted in NetCDF format and analyzed with AMDIS http://chemdata.nist.gov/mass-spc/amdis/. An home retention indices/ mass spectra library built from the NIST, Golm , http://gmd.mpimp-golm.mpg.de/ and Fiehn databases and standard compounds was used for metabolites identification. Peak areas were also determined with the Targetlynx software (Waters) after conversion of the NetCDF file in masslynx format. AMDIS, Target Lynx in splitless and split 30 modes data were compiled in one single Excel File for comparison. After blank mean substraction peak areas were normalized to Ribitol and Fresh Weight. Statistical analysis was made with TMEV http://www.tm4.org/mev.html : univariate analysis by permutation (1way-anova and 2-way anova) were firstly used to select the significant metabolites (P-value < 0.01). Multivariate analysis (hierarchical clustering an principal component analysis) were then made on them. Mapman http://www.gabipd.org/projects/MapMan/ was used for graphical representation of the metabolic changes after Log2 transformation of the mean of the 3 replicates. Absolute quantification: A response coefficient was determined for 4 ng each of a set of 103 métabolites, respectively to the same amount of ribitol. This factor was used to give an estimation of the absolute concentration of the metabolite in what we may call a “one point calibration”. Metabolites rich in nitrogen (basic aminoacids and polyamines) gave several analytes (up to 5 for glutamine and asparagine). The peak area as TIC equivalent of these analytes were summed to express the contents of these metabolites. They are referred to “sum” in the tables.
Ion Mode:POSITIVE
Helium Flow:0.7 ml/min
Ion Source Temperature:250
Ionization:EI
Source Temperature:250
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