Summary of Study ST004040

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 PR002532. The data can be accessed directly via it's Project DOI: 10.21228/M8BZ6X 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.

Study ID	ST004040
Study Title	Metabolic transitions during germination sensu stricto in Lentil (Lens culinaris cv. Anicia) seeds under two temparature regimes.
Study Type	Research
Study Summary	Germination and metabolomic analyses were performed on Lens culinaris cv. Anicia seeds at 25°C and 30°C to study temperature-dependent germination kinetics and associated metabolic changes. Seeds were obtained from Agri-Obtentions (France) and germinated using the EasyGreen Light automatic sprouter under continuous light (200 μmol·m⁻²·s⁻¹). After a 4-hour soak in water (2× dry weight), seeds were transferred to trays with 100% humidity. Germination was defined as radicle emergence of at least 2 mm, and kinetics were tracked to determine the time to 1% germination (T₁% = 12 h) and 90% germination (T₉₀% = 24 h). For metabolomic analysis, dry seeds (DS), early imbibed seeds at T₁% (EI 25°C, EI 30°C), and late imbibed seeds at T₉₀% (LI 25°C, LI 30°C) were processed. Samples (three biological replicates per condition) were ground in liquid nitrogen, lyophilized, and extracted using water/acetonitrile/isopropanol (2:3:3, −20°C) containing ribitol as an internal standard. After centrifugation and drying, extracts were derivatized with methoxyamine in pyridine and MSTFA, then analyzed using an Agilent 7890A GC coupled to a 5975C MS with an Rxi-5SilMS column. GC–MS conditions included a temperature ramp from 70°C to 325°C, helium flow at 1.52 mL/min, and a scan rate of 5 scans per second. Data were converted to NetCDF format, processed with AMDIS, and metabolites were identified using a custom RI/mass spectral library. Quantification was performed using QuanLynx after conversion to MassLynx format. A total of 300 metabolites were quantified using GC-MS, of which 124 metabolites were identified.
Institute	INRAE
Department	IJPB/Institut Jean-Pierre Bourgin, INRAE-AgroParisTech
Laboratory	Physiology of germination
Last Name	RAJJOU
First Name	Loïc
Address	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email	loic.rajjou@inrae.fr
Phone	+33 (0) 1 30 83 38 91
Submit Date	2025-02-20
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2025-07-21
Release Version	1

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Project:

Project ID:	PR002532
Project DOI:	doi: 10.21228/M8BZ6X
Project Title:	Metabolic transitions during germination sensu stricto in Lentil (Lens culinaris cv. Anicia) seeds under two temparature regimes.
Project Type:	Research
Project Summary:	Lentils (Lens culinaris), a staple crop in the Fabaceae family, are widely recognized for their high protein content, rich nutritional value, and agronomic importance. Despite their early domestication and global significance, lentils have not received the same level of research investment as other legumes, particularly in systems biology approaches. Seed germination, especially germination sensu stricto—the phase from water uptake by the dry seed to radicle protrusion—is a critical developmental stage marked by profound metabolic reprogramming. In this study, we investigated the metabolic transitions occurring during germination sensu stricto in the ANICIA lentil variety, a prominent French cultivar with Protected Designation of Origin status. Using a metabolomics approach, we analyzed dry and germinating seeds under two temperature conditions (25°C and 30°C) to characterize the dynamic biochemical changes involved in the early stages of germination.
Institute:	INRAE
Department:	IJPB/Institut Jean-Pierre Bourgin, INRAE-AgroParisTech
Laboratory:	Physiology of germination
Last Name:	Rajjou
First Name:	Loïc
Address:	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email:	loic.rajjou@inrae.fr
Phone:	+33 (0) 1 30 83 38 91

Subject:

Subject ID:	SU004186
Subject Type:	Plant
Subject Species:	Lens culinaris
Taxonomy ID:	3864
Genotype Strain:	Anicia

Factors:

Subject type: Plant; Subject species: Lens culinaris (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Imbibition	Temperature
SA467041	Lens_25°C_12h_1	Seeds	12 H	25°C
SA467042	Lens_25°C_12h_2	Seeds	12 H	25°C
SA467043	Lens_25°C_12h_3	Seeds	12 H	25°C
SA467044	Lens_25°C_24h_1	Seeds	24 H	25°C
SA467045	Lens_25°C_24h_2	Seeds	24 H	25°C
SA467046	Lens_25°C_24h_3	Seeds	24 H	25°C
SA467047	Lens_30°C_24h_1	Seeds	24 H	30°C
SA467048	Lens_30°C_24h_2	Seeds	24 H	30°C
SA467049	Lens_30°C_24h_3	Seeds	24 H	30°C
SA467050	Lens_30°C_8h_1	Seeds	8 H	30°C
SA467051	Lens_30°C_8h_2	Seeds	8 H	30°C
SA467052	Lens_30°C_8h_3	Seeds	8 H	30°C
SA467053	Lens_Dry_1	Seeds	Control	Dry
SA467054	Lens_Dry_2	Seeds	Control	Dry
SA467055	Lens_Dry_3	Seeds	Control	Dry

Showing results 1 to 15 of 15

Showing results 1 to 15 of 15

Collection:

Collection ID:	CO004179
Collection Summary:	Lentil (Lens culinaris cv. Anicia) seeds were obtained from Agri-Obtentions (Guyancourt, Yvelines, France). After imbibition, the seeds were placed on trays and relative humidity was maintained at 100%. A seed was considered germinated when the radicle protruded 2 mm from the seed coat. The germinated seeds were manually ground in liquid nitrogen into a fine powder using a mortar and pestel before lyophilization. The frozen ground samples were stored at -80°C.
Sample Type:	Seeds
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004195
Treatment Summary:	Lentil (Lens culinaris cv. Anicia) seeds obtained from Agri-Obtentions (Guyancourt, Yvelines, France) were used. Germination experiments were conducted in a growth chamber using the EasyGreen Light automatic sprouter(EasyGreen® Factory Inc., Nevada, USA) under continuous light (OSRAM Lumilux L36W/865 Cool Daylight; 200 μmol m⁻² s⁻¹). The seeds were fully immersed in Falcon tubes for 4 hours in water at a volume twice their dry weight. After imbibition, the seeds were placed on trays, and relative humidity was maintained at 100% using the misting system of the EasyGreen device. A seed was considered germinated when the radicle protruded 2 mm from the seed coat. For germination experiments conducted at 25 °C and 30 °C, germination kinetics were monitored precisely to determine the time required to reach 1% (T1%) and 90% (T90%) germination. A metabolomic analysis was performed on: •Dry seeds (DS) •Early imbibed seeds at 25 °C (EI 25 °C) and 30 °C (EI 30 °C) (T1%) •Late imbibed seeds at 25 °C (LI 25 °C) and 30 °C (LI 30 °C) (T90%) For metabolomic analysis, three biological replicates of dry and germinating lentil seeds were manually ground in liquid nitrogen into a fine powder using a mortar and pestle before lyophilization. The frozen ground samples were stored at -80°C.

Treatment ID:

TR004195

Treatment Summary:

Lentil (Lens culinaris cv. Anicia) seeds obtained from Agri-Obtentions (Guyancourt, Yvelines, France) were used. Germination experiments were conducted in a growth chamber using the EasyGreen Light automatic sprouter(EasyGreen® Factory Inc., Nevada, USA) under continuous light (OSRAM Lumilux L36W/865 Cool Daylight; 200 μmol m⁻² s⁻¹). The seeds were fully immersed in Falcon tubes for 4 hours in water at a volume twice their dry weight. After imbibition, the seeds were placed on trays, and relative humidity was maintained at 100% using the misting system of the EasyGreen device. A seed was considered germinated when the radicle protruded 2 mm from the seed coat. For germination experiments conducted at 25 °C and 30 °C, germination kinetics were monitored precisely to determine the time required to reach 1% (T1%) and 90% (T90%) germination. A metabolomic analysis was performed on: •Dry seeds (DS) •Early imbibed seeds at 25 °C (EI 25 °C) and 30 °C (EI 30 °C) (T1%) •Late imbibed seeds at 25 °C (LI 25 °C) and 30 °C (LI 30 °C) (T90%) For metabolomic analysis, three biological replicates of dry and germinating lentil seeds were manually ground in liquid nitrogen into a fine powder using a mortar and pestle before lyophilization. The frozen ground samples were stored at -80°C.

Sample Preparation:

Sampleprep ID:	SP004192
Sampleprep Summary:	For metabolite profiling, three biological replicates of 20mg of dried or germinating lentil seeds flour were used. The frozen ground samples were stored at -80 °C and later resuspended in 1 mL of water/acetonitrile/isopropanol (2:3:3 v/v/v) at -20 °C, supplemented with Ribitol (4 µg/mL) as an internal standard. Extraction was performed at 4 °C, shaking at 1400 rpm for 10 minutes in an Eppendorf Thermomixer (Eppendorf). After centrifugation at 20,000× g for 5 minutes, insoluble material was removed. A 25 µL aliquot of the extract was dried for 150 minutes using a SpeedVac (Savant SPD131DDA, Thermo Fisher Scientific, Waltham, MA, USA) and stored at -80 °C. Before further analysis, samples were thawed at room temperature for 15 minutes, then dried for another hour in the SpeedVac.

Sampleprep ID:

SP004192

Sampleprep Summary:

For metabolite profiling, three biological replicates of 20mg of dried or germinating lentil seeds flour were used. The frozen ground samples were stored at -80 °C and later resuspended in 1 mL of water/acetonitrile/isopropanol (2:3:3 v/v/v) at -20 °C, supplemented with Ribitol (4 µg/mL) as an internal standard. Extraction was performed at 4 °C, shaking at 1400 rpm for 10 minutes in an Eppendorf Thermomixer (Eppendorf). After centrifugation at 20,000× g for 5 minutes, insoluble material was removed. A 25 µL aliquot of the extract was dried for 150 minutes using a SpeedVac (Savant SPD131DDA, Thermo Fisher Scientific, Waltham, MA, USA) and stored at -80 °C. Before further analysis, samples were thawed at room temperature for 15 minutes, then dried for another hour in the SpeedVac.

Chromatography:

Chromatography ID:	CH005075
Chromatography Summary:	The instrument was an Agilent 7890A gas chromatograph coupled to an Agilent 5975C mass spectrometer.The column was an Rxi-5SilMS from Restek (30 m with 10 m integra-guard column). Before each series of analysis, the liner (Restek # 20994) was replaced and 10 cm of the column was trimmed. Oven temperature program was as follow: initial temperature was 70°C for 7 minutes, temperature ramp increase by 10°C/minute to 325°C and the final hold was 325°C for 4 minutes which brings the total run lenght to 36.5 minutes. Helium constant flow was set at 1.52 mL/min. The temperature settings were the following: - Injector: 250°C - Transfer line: 290°C - Ion source: 250°C - Quadrupole: 150°C. 5 scans per second were acquired.
Instrument Name:	Agilent 7890A
Column Name:	Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
Column Temperature:	Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 330 °C for 5 min (run length 38 min)
Flow Gradient:	NA
Flow Rate:	1.52 mL/min
Solvent A:	NA
Solvent B:	NA
Chromatography Type:	GC

Analysis:

Analysis ID:	AN006679
Analysis Type:	MS
Chromatography ID:	CH005075
Num Factors:	5
Num Metabolites:	300
Units:	µg/mg Dry Weight