#METABOLOMICS WORKBENCH MicrometaboliteNR_20240105_093107 DATATRACK_ID:4560 STUDY_ID:ST003041 ANALYSIS_ID:AN004988 PROJECT_ID:PR001283
VERSION             	1
CREATED_ON             	January 11, 2024, 8:17 am
#PROJECT
PR:PROJECT_TITLE                 	MICROMETABOLITE
PR:PROJECT_SUMMARY               	The overall objective of MICROMETABOLITE is to explore interactions between
PR:PROJECT_SUMMARY               	plants and microorganisms involved in the production of secondary metabolites
PR:PROJECT_SUMMARY               	(SM) for introducing novel ingredients in pharmaceutical and cosmeceutical
PR:PROJECT_SUMMARY               	industry. Effects of microorganisms on the plant metabolome and the biosynthesis
PR:PROJECT_SUMMARY               	of bioactive SM will be studied in the Boraginaceae plant family, aimed at
PR:PROJECT_SUMMARY               	optimising plant cultivation and alkannins/shikonins (A/S) production.
PR:PROJECT_SUMMARY               	Microorganisms will be integrated in plant production systems, and protocols
PR:PROJECT_SUMMARY               	needed for efficient implementation in industry will be elaborated. Thereby a
PR:PROJECT_SUMMARY               	platform will be established that will support long-term interactions between
PR:PROJECT_SUMMARY               	academia and industry.
PR:INSTITUTE                     	Aristotle University of Thessaloniki
PR:DEPARTMENT                    	School of Chemical Engineering
PR:LAST_NAME                     	Rodić
PR:FIRST_NAME                    	Nebojša
PR:ADDRESS                       	Stepe Stepanovića 5, Čonoplja, Vojvodina, Serbia
PR:EMAIL                         	nebojsa.rodic@hotmail.com
PR:PHONE                         	+381648766400
PR:FUNDING_SOURCE                	Horizon 2020
PR:PROJECT_COMMENTS              	This research was supported by the European Union's Horizon 2020 research and
PR:PROJECT_COMMENTS              	innovation programme under the Marie Skłodowska-Curie grant agreement No 721635
#STUDY
ST:STUDY_TITLE                   	Soil pH, developmental stages and geographical origin differently influence the
ST:STUDY_TITLE                   	root metabolomic diversity and root-related microbial diversity of Echium
ST:STUDY_TITLE                   	vulgare from native habitats
ST:STUDY_SUMMARY                 	This study examines the impact of different factors (geographic location, soil
ST:STUDY_SUMMARY                 	pH, genetic cluster, developmental stage) on the metabolome and microbiome of
ST:STUDY_SUMMARY                 	wild Echium vulgare, as well as the microbiome-metabolome correlation contained
ST:STUDY_SUMMARY                 	therein. Samples analyzed are wild Echium vulgare plant roots collected at six
ST:STUDY_SUMMARY                 	locations in Austria; out of the six locations, four contain plant roots from
ST:STUDY_SUMMARY                 	two different developmental stages. Extraction of metabolites and subsequent
ST:STUDY_SUMMARY                 	UHPLC-HRMS analysis were performed to obtain data for metabolomics analysis.
ST:INSTITUTE                     	Aristotle University of Thessaloniki
ST:LAST_NAME                     	Rodić
ST:FIRST_NAME                    	Nebojša
ST:ADDRESS                       	Stepe Stepanovića 5, Čonoplja, Vojvodina, Serbia
ST:EMAIL                         	nebojsa.rodic@hotmail.com
ST:PHONE                         	+381648766400
#SUBJECT
SU:SUBJECT_TYPE                  	Plant
SU:SUBJECT_SPECIES               	Echium vulgare
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	EV_A1	Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_A1.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_A2	Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_A2.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_A3	Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_A3.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_A4	Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_A4.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_A5	Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_A5.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AI	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AII	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AIV	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AV	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AVI	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AVII	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AVII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_AVIII	Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_AVIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B1	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B1.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B2	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B2.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B3	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B3.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B4	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B4.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B5	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B5.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_B6	Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_B6.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BI	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BII	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BIII	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BIV	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BV	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_BVI	Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1	Sample type=sample; RAW_FILE_NAME=EV_BVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C1	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C1.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C2	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C2.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C3	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C3.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C4	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C4.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C5	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C5.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_C6	Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_C6.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CI	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CII	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CIII	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CIV	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CV	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_CVI	Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_CVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EI	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EII	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EIII	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EIV	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EV	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_EVI	Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_EVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F1	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F1.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F2	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F2.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F3	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F3.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F4	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F4.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F5	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F5.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_F6	Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_F6.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FI	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FII	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FIII	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FIV	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FV	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_FVI	Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_FVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GI	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GII	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GIII	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GIII.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GIV	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GIV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GV	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GV.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GVI	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GVI.raw
SUBJECT_SAMPLE_FACTORS           	-	EV_GVII	Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2	Sample type=sample; RAW_FILE_NAME=EV_GVII.raw
SUBJECT_SAMPLE_FACTORS           	-	QC_EV_02	Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA	Sample type=QC; RAW_FILE_NAME=QC_EV_02.raw
SUBJECT_SAMPLE_FACTORS           	-	QC_EV_03	Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA	Sample type=QC; RAW_FILE_NAME=QC_EV_03.raw
SUBJECT_SAMPLE_FACTORS           	-	QC_EV	Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA	Sample type=QC; RAW_FILE_NAME=QC_EV.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	Echium vulgare plants were collected in six locations in Austria. Four of the
CO:COLLECTION_SUMMARY            	locations contained both rosette-stage and flowering plants, while two of the
CO:COLLECTION_SUMMARY            	remaining locations contained only rosette-stage plants. Roots of the plants
CO:COLLECTION_SUMMARY            	were collected and subsequently analyzed.
CO:SAMPLE_TYPE                   	Plant roots
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	After the collection, no additional treatment except for the cutting of roots
TR:TREATMENT_SUMMARY             	was performed. The roots were split into parts for various microbiological
TR:TREATMENT_SUMMARY             	analyses and parts for metabolomics analysis.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Plant roots were ground to a fine powder using a ball mill (Fritsch Pulverisette
SP:SAMPLEPREP_SUMMARY            	0, Germany). Each powdered sample was weighed (70 mg) into microcentrifuge
SP:SAMPLEPREP_SUMMARY            	tubes, followed by extraction with 3 mL of methanol by ultrasound at 10% power
SP:SAMPLEPREP_SUMMARY            	for 3 h (Bandelin Sonorex Digital 10P, Berlin, Germany) and centrifugation for
SP:SAMPLEPREP_SUMMARY            	10 minutes at 12.500 rpm (Hermle Z 216 MK, Wehingen, Germany). The supernatants
SP:SAMPLEPREP_SUMMARY            	were collected and subjected to UHPLC-HRMS analysis after filtering with 0.22
SP:SAMPLEPREP_SUMMARY            	μm syringe filters.
SP:PROCESSING_STORAGE_CONDITIONS 	-80℃
SP:EXTRACT_STORAGE               	Room temperature
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Accela AS
CH:COLUMN_NAME                   	Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um)
CH:SOLVENT_A                     	Ultrapure water (0.1% formic acid)
CH:SOLVENT_B                     	LCMS-grade methanol (0.1% formic acid)
CH:FLOW_GRADIENT                 	0 min 95A/5B, 1 min 50A/50B, 8 min 0A/100B, 13 min 0A/100B, 13.01 min 95A/5B, 16
CH:FLOW_GRADIENT                 	min 95A/5B
CH:FLOW_RATE                     	0.3 mL/min
CH:COLUMN_TEMPERATURE            	50
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo LTQ Discovery Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	The MS/MS data were obtained for the six most intense m/z peaks in each full
MS:MS_COMMENTS                   	scan, with the normalized collision energy set to 35 eV. The acquisition and
MS:MS_COMMENTS                   	initial processing of the data were by means of XcaliburTM (Thermo Scientific,
MS:MS_COMMENTS                   	USA) software, while data alignment and feature extraction were performed
MS:MS_COMMENTS                   	utilizing the XCMS Online platform (The Scripps Research Institute, USA).
MS:MS_RESULTS_FILE               	ST003041_AN004988_Results.txt	UNITS:Intensity	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END