#METABOLOMICS WORKBENCH ManoelSouza_20220928_093934 DATATRACK_ID:3479 STUDY_ID:ST002429 ANALYSIS_ID:AN003953 PROJECT_ID:PR001563
VERSION             	1
CREATED_ON             	January 5, 2023, 5:02 pm
#PROJECT
PR:PROJECT_TITLE                 	Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis
PR:PROJECT_TITLE                 	guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity
PR:PROJECT_TYPE                  	Multi-Omics Integration (MOI) Study
PR:PROJECT_SUMMARY               	Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed
PR:PROJECT_SUMMARY               	vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where
PR:PROJECT_SUMMARY               	it meets its natural condition of high rainfall throughout the year. The palm
PR:PROJECT_SUMMARY               	oil industry faces criticism due to a series of practices that was considered
PR:PROJECT_SUMMARY               	not environmentally sustainable, and it finds itself under pressure to adopt new
PR:PROJECT_SUMMARY               	and innovative procedures to reverse this negative public perception.
PR:PROJECT_SUMMARY               	Cultivating this oilseed crop outside the rainforest zone is only possible using
PR:PROJECT_SUMMARY               	artificial irrigation. Close to 30% of the world’s irrigated agricultural
PR:PROJECT_SUMMARY               	lands also face problems due to salinity stress. Consequently, the research
PR:PROJECT_SUMMARY               	community must consider drought and salinity together when studying to empower
PR:PROJECT_SUMMARY               	breeding programs in order to develop superior genotypes adapted to those
PR:PROJECT_SUMMARY               	potential new areas for oil palm cultivation. Multi-Omics Integration (MOI)
PR:PROJECT_SUMMARY               	offers a new window of opportunity for the non-trivial challenge of unraveling
PR:PROJECT_SUMMARY               	the mechanisms behind multigenic traits, such as drought and salinity tolerance.
PR:PROJECT_SUMMARY               	The current study carried out a comprehensive, large-scale, single-omics
PR:PROJECT_SUMMARY               	analysis (SOA), and MOI study on the leaves of young oil palm plants submitted
PR:PROJECT_SUMMARY               	to very high salinity stress. Taken together, a total of 1239 proteins were
PR:PROJECT_SUMMARY               	positively regulated, and 1660 were negatively regulated in transcriptomics and
PR:PROJECT_SUMMARY               	proteomics analyses. Meanwhile, the metabolomics analysis revealed 37
PR:PROJECT_SUMMARY               	metabolites that were upreg- ulated and 92 that were downregulated. After
PR:PROJECT_SUMMARY               	performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE
PR:PROJECT_SUMMARY               	proteins, and 19 DE metabolites underwent MOI analysis, revealing sev- eral
PR:PROJECT_SUMMARY               	pathways affected by this stress, with at least one DE molecule in all three
PR:PROJECT_SUMMARY               	omics platforms used. The Cysteine and methionine metabolism (map00270) and
PR:PROJECT_SUMMARY               	Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each
PR:PROJECT_SUMMARY               	one with 20 DE molecules.
PR:INSTITUTE                     	The Brazilian Agricultural Research Corporation (Embrapa)
PR:DEPARTMENT                    	Embrapa Agroenergy
PR:LABORATORY                    	Genetics and Plant Biotechnology
PR:LAST_NAME                     	Souza Jr
PR:FIRST_NAME                    	Manoel Teixeira
PR:ADDRESS                       	Parque Estacao Biologica, Final Avenida W3 Norte - Asa Norte, Brasilia, Distrito
PR:ADDRESS                       	Federal, 70770901, Brazil
PR:EMAIL                         	manoel.souza@embrapa.br
PR:PHONE                         	+55.61.3448.3210
PR:FUNDING_SOURCE                	FINEP (01.13.0315.00)
PR:PROJECT_COMMENTS              	DendêPalm Project
PR:PUBLICATIONS                  	https://doi.org/10.3390/plants11131755
#STUDY
ST:STUDY_TITLE                   	Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis
ST:STUDY_TITLE                   	guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity
ST:STUDY_TYPE                    	Multi-Omics Integration (MOI) Study
ST:STUDY_SUMMARY                 	Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed
ST:STUDY_SUMMARY                 	vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where
ST:STUDY_SUMMARY                 	it meets its natural condition of high rainfall throughout the year. The palm
ST:STUDY_SUMMARY                 	oil industry faces criticism due to a series of practices that was considered
ST:STUDY_SUMMARY                 	not environmentally sustainable, and it finds itself under pressure to adopt new
ST:STUDY_SUMMARY                 	and innovative procedures to reverse this negative public perception.
ST:STUDY_SUMMARY                 	Cultivating this oilseed crop outside the rainforest zone is only possible using
ST:STUDY_SUMMARY                 	artificial irrigation. Close to 30% of the world’s irrigated agricultural
ST:STUDY_SUMMARY                 	lands also face problems due to salinity stress. Consequently, the research
ST:STUDY_SUMMARY                 	community must consider drought and salinity together when studying to empower
ST:STUDY_SUMMARY                 	breeding programs in order to develop superior genotypes adapted to those
ST:STUDY_SUMMARY                 	potential new areas for oil palm cultivation. Multi-Omics Integration (MOI)
ST:STUDY_SUMMARY                 	offers a new window of opportunity for the non-trivial challenge of unraveling
ST:STUDY_SUMMARY                 	the mechanisms behind multigenic traits, such as drought and salinity tolerance.
ST:STUDY_SUMMARY                 	The current study carried out a comprehensive, large-scale, single-omics
ST:STUDY_SUMMARY                 	analysis (SOA), and MOI study on the leaves of young oil palm plants submitted
ST:STUDY_SUMMARY                 	to very high salinity stress. Taken together, a total of 1239 proteins were
ST:STUDY_SUMMARY                 	positively regulated, and 1660 were negatively regulated in transcriptomics and
ST:STUDY_SUMMARY                 	proteomics analyses. Meanwhile, the metabolomics analysis revealed 37
ST:STUDY_SUMMARY                 	metabolites that were upreg- ulated and 92 that were downregulated. After
ST:STUDY_SUMMARY                 	performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE
ST:STUDY_SUMMARY                 	proteins, and 19 DE metabolites underwent MOI analysis, revealing sev- eral
ST:STUDY_SUMMARY                 	pathways affected by this stress, with at least one DE molecule in all three
ST:STUDY_SUMMARY                 	omics platforms used. The Cysteine and methionine metabolism (map00270) and
ST:STUDY_SUMMARY                 	Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each
ST:STUDY_SUMMARY                 	one with 20 DE molecules.
ST:INSTITUTE                     	The Brazilian Agricultural Research Corporation (Embrapa)
ST:DEPARTMENT                    	Embrapa Agroenergy
ST:LABORATORY                    	Genetics and Plant Biotechnology
ST:LAST_NAME                     	Souza Jr
ST:FIRST_NAME                    	Manoel Teixeira
ST:ADDRESS                       	Parque Estacao Biologica, Final Avenida W3 Norte - Asa Norte, Brasilia, Distrito
ST:ADDRESS                       	Federal, 70770901, Brazil
ST:EMAIL                         	manoel.souza@embrapa.br
ST:PHONE                         	+55.61.3448.3210
ST:PUBLICATIONS                  	https://doi.org/10.3390/plants11131755
#SUBJECT
SU:SUBJECT_TYPE                  	Plant
SU:SUBJECT_SPECIES               	Elaeis guineensis Jacq.
SU:TAXONOMY_ID                   	NCBI:txid51953
#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           	-	OilPalm_Salt_Control_07DAT_R1_POS	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R1_POS	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R2_POS	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R1_POS	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R1_POS	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R2_POS	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R2_POS	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R1_POS	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R3_POS	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R4_POS	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R3_POS	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R2_POS	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R3_POS	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R3_POS	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R4_POS	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R4_POS	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R4_POS	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R2_POS	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R3_POS	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R4_POS	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R1_POS	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R1_POS	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R2_POS	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R1_POS	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R1_POS	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R2_POS	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R2_POS	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R1_POS	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R1_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R3_POS	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R4_POS	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R3_POS	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R2_POS	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R3_POS	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R3_POS	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R4_POS	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R4_POS	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R4_POS	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R2_POS	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R2_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R3_POS	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R3_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R4_POS	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R4_POS.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R1_NEG	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R1_NEG	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R2_NEG	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R1_NEG	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R1_NEG	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R2_NEG	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R2_NEG	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R1_NEG	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R3_NEG	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_07DAT_R4_NEG	Group:7 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_07DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R3_NEG	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R2_NEG	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R3_NEG	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R3_NEG	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_07DAT_R4_NEG	Group:7 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_07DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_07DAT_R4_NEG	Group:7 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_07DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_07DAT_R4_NEG	Group:7 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_07DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R2_NEG	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R3_NEG	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_07DAT_R4_NEG	Group:7 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_07DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R1_NEG	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R1_NEG	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R2_NEG	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R1_NEG	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R1_NEG	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R2_NEG	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R2_NEG	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R1_NEG	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R1_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R3_NEG	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_15_14DAT_R4_NEG	Group:14 days	Treatment=1.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_15_14DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R3_NEG	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R2_NEG	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R3_NEG	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R3_NEG	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_20_14DAT_R4_NEG	Group:14 days	Treatment=2.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_20_14DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_10_14DAT_R4_NEG	Group:14 days	Treatment=1.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_10_14DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_05_14DAT_R4_NEG	Group:14 days	Treatment=0.5g NaCl; RAW_FILE_NAME=OilPalm_Salt_05_14DAT_R4_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R2_NEG	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R2_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R3_NEG	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R3_NEG.mzXML
SUBJECT_SAMPLE_FACTORS           	-	OilPalm_Salt_Control_14DAT_R4_NEG	Group:14 days	Treatment=0.0g NaCl; RAW_FILE_NAME=OilPalm_Salt_Control_14DAT_R4_NEG.mzXML
#COLLECTION
CO:COLLECTION_SUMMARY            	The oil palm plants used in this study were clones regenerated out of
CO:COLLECTION_SUMMARY            	embryogenic calluses obtained from the leaves of an adult plant—genotype AM33,
CO:COLLECTION_SUMMARY            	a Deli x Ghana from ASD Costa Rica, as previously reported by [6]. Before
CO:COLLECTION_SUMMARY            	starting the experiments, plants were standardized accordingly to the
CO:COLLECTION_SUMMARY            	developmental stage, size, and number of leaves. They were in the growth stage
CO:COLLECTION_SUMMARY            	known as bifid saplings, and the experiment was performed in March 2018 in a
CO:COLLECTION_SUMMARY            	greenhouse at Embrapa Agroenergy in Brasília, DF, Brazil (S-15.732°,
CO:COLLECTION_SUMMARY            	W-47.900°). The main environmental variables (temperature, humidity, and
CO:COLLECTION_SUMMARY            	radiation) fluctuated according to the weather conditions and underwent
CO:COLLECTION_SUMMARY            	monitoring throughout the entire experimental period using the data collected at
CO:COLLECTION_SUMMARY            	a nearby meteorological station (S-15.789°, W-47.925°). We collected the
CO:COLLECTION_SUMMARY            	apical leaves from control and stressed plants (0.0 and 2.0 g of NaCl per 100 g
CO:COLLECTION_SUMMARY            	of substrate) 12 days after imposition of the treatments (DAT).
CO:SAMPLE_TYPE                   	Plant
#TREATMENT
TR:TREATMENT_SUMMARY             	The experiment consisted of five salinity levels (0.0, 0.5, 1.0, 1.5, and 2.0 g
TR:TREATMENT_SUMMARY             	of NaCl per 100 g of substrate (a mixture of vermiculite, soil, and the Bioplant
TR:TREATMENT_SUMMARY             	commercial substrate (Bioplant Agrícola Ltd.a., Nova Ponte, MG, Brazil), in a
TR:TREATMENT_SUMMARY             	1:1:1 ratio, on a dry basis), with four replicates in a completely randomized
TR:TREATMENT_SUMMARY             	design. The substrate mixture was fertilized using 2.5 g L−1 of the N-P2O5-K2O
TR:TREATMENT_SUMMARY             	formula (20-20-20).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Leaves harvested from control and stressed plants were immediately immersed in
SP:SAMPLEPREP_SUMMARY            	liquid nitrogen and stored at −80 °C until metabolite extraction: four plants
SP:SAMPLEPREP_SUMMARY            	for treatments. Before solvent extraction, all samples underwent grounding in
SP:SAMPLEPREP_SUMMARY            	liquid nitrogen. The solvents used were methanol grade UHPLC, acetonitrile grade
SP:SAMPLEPREP_SUMMARY            	LC-MS, formic acid grade LC-MS, sodium hydroxide ACS grade LC-MS, all from
SP:SAMPLEPREP_SUMMARY            	Sigma-Aldrich, and water treated in a Milli-Q system from Millipore. We employed
SP:SAMPLEPREP_SUMMARY            	a protocol to extract the metabolites in three phases (polar, non-polar, and
SP:SAMPLEPREP_SUMMARY            	protein pellet). Aliquots of 50 mg of ground sample were transferred to 2 mL
SP:SAMPLEPREP_SUMMARY            	microtubes, and then 1 mL of a mixture of 1:3 (v:v) methanol/methyl tert-butyl
SP:SAMPLEPREP_SUMMARY            	ether (MTBE) at −20 °C was added. Homogenization on an orbital shaker at 4.0
SP:SAMPLEPREP_SUMMARY            	°C and ultrasound treatment in an ice bath were each performed for 10 min. As
SP:SAMPLEPREP_SUMMARY            	the next step, we added 500 μL of a mixture of 1:3 (v:v) methanol/water to each
SP:SAMPLEPREP_SUMMARY            	microtube. After centrifugation (15,300× g at 4.0 °C for 5 min), an upper
SP:SAMPLEPREP_SUMMARY            	non-polar (green) and a lower polar (brown) phase and a protein pellet remained
SP:SAMPLEPREP_SUMMARY            	in each microtube. After transferring both fractions separately to 1.5 mL
SP:SAMPLEPREP_SUMMARY            	microtubes, they were submitted to a Speed vac system (Centrivap, Labconco) to
SP:SAMPLEPREP_SUMMARY            	be vacuum dried. Finally, the dry-fraction, resuspended in 500 μL of 1:3 (v:v)
SP:SAMPLEPREP_SUMMARY            	methanol and water mixture and transferred to vials, were now ready for
SP:SAMPLEPREP_SUMMARY            	analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Solvent A was 0.1% (v:v) formic acid in water and solvent B was 0.1% (v:v)
CH:CHROMATOGRAPHY_SUMMARY        	formic acid in acetonitrile/methanol (70:30, v:v). The gradient elution used,
CH:CHROMATOGRAPHY_SUMMARY        	with a flow rate of 0.4 mL min–1, was as follows: 0–1 min isocratic, 0% B;
CH:CHROMATOGRAPHY_SUMMARY        	1–3 min, 5% B; 3–10 min, 50% B; 10–13 min, 100% B; 13–15 min isocratic,
CH:CHROMATOGRAPHY_SUMMARY        	100% B; then, 5 min rebalancing was conducted to the initial conditions.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Shimadzu Nexera X2
CH:COLUMN_NAME                   	Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)
CH:SOLVENT_A                     	100% water; 0.1% formic acid
CH:SOLVENT_B                     	70% acetonitrile/30% methanol; 0.1% formic acid
CH:FLOW_GRADIENT                 	0–1 min isocratic, 0% B; 1–3 min, 5% B; 3–10 min, 50% B; 10–13 min, 100%
CH:FLOW_GRADIENT                 	B; 13–15 min isocratic, 100% B; then, 5 min rebalancing was conducted to the
CH:FLOW_GRADIENT                 	initial conditions.
CH:FLOW_RATE                     	0.4 mL/min
CH:COLUMN_TEMPERATURE            	-
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Bruker maXis Impact qTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	The rate of acquisition spectra was 3.00 Hz, mass range m/z 70–1200 for the
MS:MS_COMMENTS                   	polar fraction analysis and m/z 300–1600 for the lipidic fraction.
MS:MS_COMMENTS                   	High-resolution mass spectrometry was used for detection (MaXis 4G Q-TOF MS,
MS:MS_COMMENTS                   	Bruker Daltonics) equipped with an electrospray source in positive (ESI-(+)-MS)
MS:MS_COMMENTS                   	and negative (ESI-(−)-MS) modes. The settings of the mass spectrometer were as
MS:MS_COMMENTS                   	follows: capillary voltage, 3800 V; dry gas flow, 9 L min−1; dry temperature,
MS:MS_COMMENTS                   	200 °C; nebulizer pressure, 4 bar; final plate offset, 500 V. For the external
MS:MS_COMMENTS                   	calibration of the equipment, we used a sodium formate solution (10 mM HCOONa
MS:MS_COMMENTS                   	solution in 50:50 v:v isopropanol and water containing 0.2% formic acid)
MS:MS_COMMENTS                   	injected through a six-way valve at the beginning of each chromatographic run.
MS:MS_COMMENTS                   	Ampicillin ([M+H] + m/z 350.1186729 and [M-H]- m/z 348.1028826) was the internal
MS:MS_COMMENTS                   	standard for later peak normalization on data analysis.
MS:MS_RESULTS_FILE               	ST002429_AN003953_Results.txt	UNITS:Peak intensity	Has m/z:Yes	Has RT:No	RT units:No RT data
#END