{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002060","ANALYSIS_ID":"AN003354","VERSION":"1","CREATED_ON":"January 18, 2022, 9:05 am"},

"PROJECT":{"PROJECT_TITLE":"Pollen metabolomics using Arabidopsis thaliana: Comparison of pollen at mature, hydration and germination stage","PROJECT_TYPE":"Untargeted Metabolomics","PROJECT_SUMMARY":"Pollen germination is an essential process for pollen tube growth, pollination, and therefore seed production in flowing plants, which requires energy either from remobilization of stored carbon sources, lipid and starch, or from secreted exudates from stigma. Transcriptome analysis from in vitro pollen germination previously showed 14 GO terms, including metabolism and energy, which are overrepresented in Arabidopsis. However, the global changes of carbohydrate and energy-related metabolites during the transition from mature pollen grain to hydrated pollen, the prerequisite step to pollen germination, is poorly understood in Arabidopsis. In this study, we investigated the differential metabolic pathway enrichment among mature, hydrated, and germinated pollen using untargeted metabolomics analysis. Integration of publicly available transcriptome with presented metabolome data revealed starch and sucrose metabolism was significantly increased during pollen hydration and germination. The alterations in central metabolism focusing on sugar, fatty acids, and lipids were analyzed in detail. Several metabolites, including palmitic acid, oleic acid, linolenic acid, quercetin, luteolin/kaempferol, and γ-aminobutyric acid (GABA), were elevated in the hydrated pollen, suggesting a potential role in activating pollen tube emergence. The metabolite levels of mature, hydrated, and germinated pollen, presented in this work provide insights on the molecular basis of pollen germination.","INSTITUTE":"Donald Danforth Plant Science Center","DEPARTMENT":"Allen/USDA lab","LABORATORY":"Doug K. Allen","LAST_NAME":"Kambhampati","FIRST_NAME":"Shrikaar","ADDRESS":"975 North Warson Road, St. Louis, MO 63132","EMAIL":"shrikaar.k@gmail.com","PHONE":"3144025550","FUNDING_SOURCE":"NIH, USDA-ARS","CONTRIBUTORS":"Shrikaar Kambhampati, Jiang Wang, Doug Allen, Li-Qing Chen"},

"STUDY":{"STUDY_TITLE":"Pollen metabolomics using Arabidopsis thaliana: Comparison of pollen at mature, hydration and germination stage","STUDY_TYPE":"Untargeted Metabolomics","STUDY_SUMMARY":"In this study, we investigated the differential metabolic pathway enrichment among mature, hydrated, and germinated pollen using untargeted metabolomics analysis. Integration of publicly available transcriptome with presented metabolome data revealed starch and sucrose metabolism was significantly increased during pollen hydration and germination. The alterations in central metabolism focusing on sugar, fatty acids, and lipids were analyzed in detail. Several metabolites, including palmitic acid, oleic acid, linolenic acid, quercetin, luteolin/kaempferol, and γ-aminobutyric acid (GABA), were elevated in the hydrated pollen, suggesting a potential role in activating pollen tube emergence. The metabolite levels of mature, hydrated, and germinated pollen, presented in this work provide insights on the molecular basis of pollen germination.","INSTITUTE":"University of Illinois, Urbana-Champaign","DEPARTMENT":"Department of Plant Biology","LABORATORY":"Li-Qing Chen Lab","LAST_NAME":"Kambhampati","FIRST_NAME":"Shrikaar","ADDRESS":"975 North Warson Road, St. Louis, MO 63132","EMAIL":"shrikaar.k@gmail.com","PHONE":"3144025550","NUM_GROUPS":"3","TOTAL_SUBJECTS":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Arabidopsis thaliana","TAXONOMY_ID":"3702","GENOTYPE_STRAIN":"Col-0","AGE_OR_AGE_RANGE":"Mature pollen, Pollen hydration Stage (45 min), Pollen germination stage (4 hours)","SPECIES_GROUP":"Pollen"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Pos_1",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Pos_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Neg_1",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Neg_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Pos_2",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Pos_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Neg_2",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Neg_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Pos_3",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Pos_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Neg_3",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Neg_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Pos_4",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Pos_4"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_HILIC_Neg_4",
"Factors":{"Stage":"Mature","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_HILIC_Neg_4"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Pos_1",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Pos_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Neg_1",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Neg_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Pos_2",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Pos_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Neg_2",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Neg_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Pos_3",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Pos_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Neg_3",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Neg_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Pos_4",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Pos_4"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_RPLC_Neg_4",
"Factors":{"Stage":"Mature","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_RPLC_Neg_4"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Pos_1",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Pos_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Neg_1",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Neg_1"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Pos_2",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Pos_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Neg_2",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Neg_2"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Pos_3",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Pos_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Neg_3",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Neg_3"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Pos_4",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Pos_4"}
},
{
"Subject ID":"Control",
"Sample ID":"Mature_Lipids_Neg_4",
"Factors":{"Stage":"Mature","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Mature_Lipid_Neg_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Pos_1",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Pos_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Neg_1",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Neg_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Pos_2",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Pos_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Neg_2",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Neg_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Pos_3",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Pos_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Neg_3",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Neg_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Pos_4",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Pos_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_HILIC_Neg_4",
"Factors":{"Stage":"Hydration","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_HILIC_Neg_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Pos_1",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Pos_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Neg_1",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Neg_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Pos_2",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Pos_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Neg_2",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Neg_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Pos_3",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Pos_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Neg_3",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Neg_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Pos_4",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Pos_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_RPLC_Neg_4",
"Factors":{"Stage":"Hydration","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_RPLC_Neg_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Pos_1",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Pos_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Neg_1",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Neg_1"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Pos_2",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Pos_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Neg_2",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Neg_2"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Pos_3",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Pos_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Neg_3",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Neg_3"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Pos_4",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Pos_4"}
},
{
"Subject ID":"45 min Sucr",
"Sample ID":"Hydrated_Lipids_Neg_4",
"Factors":{"Stage":"Hydration","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Hydr_Lipid_Neg_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Pos_1",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Pos_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Neg_1",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Neg_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Pos_2",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Pos_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Neg_2",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Neg_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Pos_3",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Pos_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Neg_3",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Neg_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Pos_4",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Pos_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_HILIC_Neg_4",
"Factors":{"Stage":"Germination","Chromatography":"HILIC","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_HILIC_Neg_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Pos_1",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Pos_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Neg_1",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Neg_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Pos_2",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Pos_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Neg_2",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Neg_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Pos_3",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Pos_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Neg_3",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Neg_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Pos_4",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Pos_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_RPLC_Neg_4",
"Factors":{"Stage":"Germination","Chromatography":"RPLC (C18)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_RPLC_Neg_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Pos_1",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Pos_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Neg_1",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Neg_1"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Pos_2",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Pos_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Neg_2",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Neg_2"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Pos_3",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Pos_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Neg_3",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Neg_3"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Pos_4",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Positive"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Pos_4"}
},
{
"Subject ID":"4 Hr Sucr",
"Sample ID":"Germinated_Lipids_Neg_4",
"Factors":{"Stage":"Germination","Chromatography":"Lipidomics (C8)","Polarity":"Negative"},
"Additional sample data":{"RAW_FILE_NAME":"Col0_Germ_Lipid_Neg_4"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The Arabidopsis Col-0 plants were grown under controlled temperature (22°C) with a 16-h light (100-150 µmol m-2 s-1)/ 8-h dark photoperiod. Mature pollen grains from the fully opened flowers were collected from more than 1000 plants using a vacuum cleaner method (Johnson-Brousseau and McCormick, 2004) at around 5 hours into the light period. For mature pollen samples, collected pollen grains were resuspended in 2 ml of ice-cold Pollen Isolation Buffer (PIB, composed of 100 mM NaPO4, pH 7.5, 1 mM EDTA, and 0.1% (v/v) Triton X-100) right after collection followed by centrifuging at 15,000 g for 1 min (4°C). For hydrated pollen and germinated pollen samples, mature pollen grains were germinated in vitro according to a previously described pollen transcriptome study (Wang et al., 2008). In brief, pollen pellets were washed with 1 ml of liquid Pollen Germination Medium (PGM, composed of 15% (w/v) sucrose, 1.5 mM boric acid, 0.8 mM MgSO4, 1 mM KCl, 5 mM MES, 0.05% (w/v) lactalbumin hydrolysate, 10 µM myo-inositol, 5 mM CaCl2) before they were resuspended in 30 µl of liquid PGM and subsequently cultured in Petri dishes (35 mm in diameter). A 70 µm mesh was used to cover the pollen droplet to create a thin layer for optimal germination for each Petri dish. The Petri dishes were covered and placed in the dark for 45 min or 4 h and collected as hydrated pollen or germinated pollen, respectively. All pollen samples were washed by 1 ml ice-cold ddH2O three times before being stored in a -80 °C freezer.","COLLECTION_PROTOCOL_FILENAME":"PlantGrowth_PollenCollection.docx","SAMPLE_TYPE":"Plant","COLLECTION_METHOD":"Flash frozen in Liquid N2","COLLECTION_LOCATION":"University of Illinois, Urbana-Champain","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"For hydrated pollen and germinated pollen samples, mature pollen grains were germinated in vitro according to a previously described pollen transcriptome study (Wang et al., 2008). In brief, pollen pellets were washed with 1 ml of liquid Pollen Germination Medium (PGM, composed of 15% (w/v) sucrose, 1.5 mM boric acid, 0.8 mM MgSO4, 1 mM KCl, 5 mM MES, 0.05% (w/v) lactalbumin hydrolysate, 10 µM myo-inositol, 5 mM CaCl2) before they were resuspended in 30 µl of liquid PGM and subsequently cultured in Petri dishes (35 mm in diameter). A 70 µm mesh was used to cover the pollen droplet to create a thin layer for optimal germination for each Petri dish. The Petri dishes were covered and placed in the dark for 45 min or 4 h and collected as hydrated pollen or germinated pollen, respectively."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Total metabolites from pollen were extracted using a phase separation method previously described (Kambhampati et al., 2021) with slight modifications. Briefly, 20-30 mg pollen tissue, collected in Eppendorf tubes, was extracted using 700 µL of chilled 7:3 (v/v) methanol: chloroform spiked with 50 µM each of 1.4-piperazinediethanesulfonic acid (PEPES), ribitol, and norvaline as internal standards. After two metal beads were also added to the samples, they were homogenized using a Tissue-Lyser for 5 min at 30 Hz. The samples were incubated on a rotary shaker at 4°C for 2 hours after which 300 µL ddH2O was added. The samples were then centrifuged at 14,000 rpm for 10 min to achieve phase separation and the upper aqueous phase, as well as the lower organic phase, were collected separately. The aqueous phases containing polar and nonpolar metabolites were split into two equal parts and dried using a speed vacuum centrifuge (Labconco®, Kansas City, USA). The two dried parts were re-suspended in 50 µL 80% (v/v) methanol, and 30 % (v/v) methanol for metabolomics analyses using hydrophilic interaction (HILIC) and reverse phase chromatography (RPLC), respectively. The organic phase was also dried using a speed vacuum centrifuge and re-suspended in 50 µL of 49:49:2 (v/v/v) mixture of acetonitrile: methanol: chloroform. All samples were filtered using a 0.8 µM PES membrane centrifuge filter (Sartorius, Goettingen, Germany) and transferred to a glass vial for injection into an LC-MS/MS system.","SAMPLEPREP_PROTOCOL_FILENAME":"Total_Metabolite_Extraction.docx","PROCESSING_STORAGE_CONDITIONS":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Eksigent Ekspert microLC 200","COLUMN_NAME":"SeQuant Zic-HILIC (150 x 0.5mm x 5um)","FLOW_RATE":"0.015","COLUMN_TEMPERATURE":"35","METHODS_FILENAME":"Chromatography_PollentMetabolomics.docx","SOLVENT_A":"10 mM ammonium bicarbonate in ddH2O","SOLVENT_B":"10 mM ammonium bicarbonate in 95:5 (v/v) Acetonitrile: ddH2O"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ACQUISITION_PARAMETERS_FILE":"MS_DataAcquisition.docx"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"All parameters listed in the attached document","MS_RESULTS_FILE":"ST002060_AN003354_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Minutes"}

}