{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001166","ANALYSIS_ID":"AN001928","VERSION":"1","CREATED_ON":"April 9, 2019, 2:56 pm"},

"PROJECT":{"PROJECT_TITLE":"GC analysis of crab megalopae and juveniles in response to ocean acidification","PROJECT_SUMMARY":"The objective of the study was to examine the physiological and metabolic response of crab megalopae and juveniles to ocean acidification treatment.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258"},

"STUDY":{"STUDY_TITLE":"Physiological and metabolic response of pteropods to ocean acidification (part IV)","STUDY_SUMMARY":"The objective of the study was to examine the physiological and metabolic response of pteropods to ocean acidification treatment. Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO","INSTITUTE":"NOAA NWFSC","DEPARTMENT":"CB Division","LAST_NAME":"Nichols","FIRST_NAME":"Krista","ADDRESS":"1315 East-West Highway Silver Spring, MD 20910","EMAIL":"krista.nichols@noaa.gov","PHONE":"206-302-2470","NUM_GROUPS":"4","TOTAL_SUBJECTS":"60"},

"SUBJECT":{"SUBJECT_TYPE":"Invertebrate","SUBJECT_SPECIES":"Metacarcinus magister","TAXONOMY_ID":"29965"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"M4D1",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6C7",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M1A7",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M1C5",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M1C7",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M1D6",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M10A6",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M10B4",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M10C3",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M10D7",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M10B1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M11A2",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M11A4",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M11B2",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M11D3",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M11D7",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12A1",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12A2",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12B2",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12B3",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12C2",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12C6",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M12D4",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M13A2",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M13B5",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M13C2",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M13D4",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M13A7",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M3A2",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M3B3",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M3C1",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M3D4",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M3A3",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M4A2",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M4B6",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M4C3",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M4D7",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M4A3",
"Factors":{"pH Treatment":"Low","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M5A1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M5B5",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M5B6",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M5C1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M5D1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M6A1",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6A2",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6B3",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6B7",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6C6",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6D2",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M6D4",
"Factors":{"pH Treatment":"High","DO Treatment":"Low"}
},
{
"Subject ID":"-",
"Sample ID":"M7A6",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M7B2",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M7C2",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M7D6",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M7C5",
"Factors":{"pH Treatment":"High","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M8A5",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M8B1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M8C1",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M8D4",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
},
{
"Subject ID":"-",
"Sample ID":"M8D6",
"Factors":{"pH Treatment":"Low","DO Treatment":"High"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After completing the required treatment time of 30-33 days, each crab was frozen at -80C and shipped to the West Coast Metabolomics Center.","SAMPLE_TYPE":"Muscle Tissue"},

"TREATMENT":{"TREATMENT_SUMMARY":"Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Crabs were removed from -80°C. 15 mg of muscle tissue was removed from each crab and placed in a 2 mL eppendorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of methanol with quality control standards were added to each sample. Samples were ground for 30 seconds at 1500 rpm using a GenoGrinder. 750 µL of methyl-tertbutyl ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaked at 4°C for 6 minutes. 188 µL of LC-MS grade water was added to each sample. Samples were vortexed for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. The top, organic layer was split into two 350 µL aliquots, one submitted to lipidomics analysis and one saved for backup. The bottom layer was split into two 125 µL aliquots, one submitted to GC analysis and one saved as a backup."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)","FLOW_RATE":"1 mL/min","COLUMN_TEMPERATURE":"50-330","INJECTION_TEMPERATURE":"50°C ramped to 250°C by 12°C s-1","SAMPLE_INJECTION":"0.5 uL","OVEN_TEMPERATURE":"50°C for 1 min, then ramped at 20°C min-1 to 330°C, held constant for 5 min"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Leco Pegasus HT TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"N/A","ION_SOURCE_TEMPERATURE":"250°C","IONIZATION_ENERGY":"-70 eV","DATAFORMAT":".peg, .txt, .cdf","RESOLUTION_SETTING":"17 spectra/sec","SCANNING_RANGE":"80-500 Da"},

"MS_METABOLITE_DATA":{
"Units":"Peak Height",

"Data":[{"Metabolite":"zymosterol","M4D1":"35500","M6C7":"33005","M1A7":"16974","M1C5":"21288","M1C7":"36578","M1D6":"18271","M10B4":"26405","M10C3":"31507","M10D7":"33615","M10B1":"59972","M11A2":"49462","M11A4":"240","M11B2":"43805","M11D3":"50765","M11D7":"21544","M12A1":"27510","M12A2":"20829","M12B2":"25238","M12B3":"35769","M12C2":"10918","M12C6":"18036","M12D4":"18771","M13A2":"28235","M13B5":"33697","M13C2":"18745","M13D4":"29334","M13A7":"36324","M3A2":"23104","M3B3":"19094","M3C1":"17283","M3D4":"15457","M3A3":"15975","M4A2":"48447","M4B6":"28770","M4C3":"28614","M4D7":"28121","M4A3":"15402","M5A1":"21773","M5B5":"27885","M5B6":"36924","M5C1":"14650","M5D1":"45043","M6A1":"16254","M6A2":"13265","M6B3":"35564","M6B7":"14692","M6C6":"8912","M6D2":"35401","M6D4":"16056","M7A6":"12571","M7B2":"27943","M7C2":"17255","M7D6":"17880","M7C5":"44727","M8A5":"17014","M8B1":"29830","M8C1":"22600","M8D4":"21888"},{"Metabolite":"xylitol","M4D1":"2465","M6C7":"169","M1A7":"201","M1C5":"125","M1C7":"186","M1D6":"280","M10B4":"139","M10C3":"3373","M10D7":"196","M10B1":"569","M11A2":"7812","M11A4":"262","M11B2":"2487","M11D3":"329","M11D7":"331","M12A1":"312","M12A2":"739","M12B2":"178","M12B3":"390","M12C2":"712","M12C6":"173","M12D4":"190","M13A2":"158","M13B5":"158","M13C2":"1795","M13D4":"168","M13A7":"261","M3A2":"238","M3B3":"253","M3C1":"382","M3D4":"337","M3A3":"162","M4A2":"238","M4B6":"115","M4C3":"1539","M4D7":"740","M4A3":"165","M5A1":"193","M5B5":"257","M5B6":"193","M5C1":"162","M5D1":"120","M6A1":"159","M6A2":"168","M6B3":"147","M6B7":"164","M6C6":"143","M6D2":"183","M6D4":"242","M7A6":"194","M7B2":"9346","M7C2":"1673","M7D6":"966","M7C5":"882","M8A5":"622","M8B1":"151","M8C1":"1070","M8D4":"203"},{"Metabolite":"valine","M4D1":"7095","M6C7":"26770","M1A7":"14619","M1C5":"14470","M1C7":"23519","M1D6":"19076","M10B4":"4438","M10C3":"18182","M10D7":"18849","M10B1":"6466","M11A2":"20649","M11A4":"959","M11B2":"12921","M11D3":"20862","M11D7":"19844","M12A1":"33805","M12A2":"8833","M12B2":"16942","M12B3":"29770","M12C2":"5707","M12C6":"20213","M12D4":"24271","M13A2":"34645","M13B5":"30818","M13C2":"24953","M13D4":"26552","M13A7":"37792","M3A2":"48309","M3B3":"22790","M3C1":"13271","M3D4":"9847","M3A3":"14471","M4A2":"23364","M4B6":"16676","M4C3":"12616","M4D7":"21508","M4A3":"13598","M5A1":"25185","M5B5":"6847","M5B6":"36738","M5C1":"12644","M5D1":"20426","M6A1":"23321","M6A2":"14309","M6B3":"35140","M6B7":"18893","M6C6":"18191","M6D2":"21990","M6D4":"28498","M7A6":"6062","M7B2":"16593","M7C2":"12233","M7D6":"10740","M7C5":"43303","M8A5":"9808","M8B1":"26545","M8C1":"10058","M8D4":"14586"},{"Metabolite":"urea","M4D1":"10311","M6C7":"48881","M1A7":"5854","M1C5":"12430","M1C7":"7747","M1D6":"35567","M10B4":"35640","M10C3":"68622","M10D7":"23708","M10B1":"21216","M11A2":"84366","M11A4":"7001","M11B2":"35504","M11D3":"1571","M11D7":"30712","M12A1":"18779","M12A2":"59327","M12B2":"14205","M12B3":"39865","M12C2":"36319","M12C6":"43669","M12D4":"28666","M13A2":"29633","M13B5":"25085","M13C2":"49278","M13D4":"31055","M13A7":"23088","M3A2":"13871","M3B3":"25146","M3C1":"42645","M3D4":"9749","M3A3":"40501","M4A2":"28786","M4B6":"38269","M4C3":"62966","M4D7":"10430","M4A3":"32213","M5A1":"31779","M5B5":"12995","M5B6":"12207","M5C1":"29519","M5D1":"27268","M6A1":"22273","M6A2":"31490","M6B3":"17393","M6B7":"34142","M6C6":"20571","M6D2":"33981","M6D4":"17400","M7A6":"33498","M7B2":"34283","M7C2":"12044","M7D6":"15140","M7C5":"22043","M8A5":"44839","M8B1":"32976","M8C1":"18494","M8D4":"28597"},{"Metabolite":"UDP 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}

}