{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000423","ANALYSIS_ID":"AN000671","VERSION":"1","CREATED_ON":"July 18, 2016, 2:23 pm"},

"PROJECT":{"PROJECT_TITLE":"Differences in mycoplasma growth due to different mediums","PROJECT_SUMMARY":"The object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesis; and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.","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","FUNDING_SOURCE":"NIH U24DK097154"},

"STUDY":{"STUDY_TITLE":"Differences in mycoplasma growth due to different mediums","STUDY_SUMMARY":"The object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesis; and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.","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","NUM_GROUPS":"4","TOTAL_SUBJECTS":"24"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Resident macrophage 1",
"Sample ID":"Quigley_Inj12_SA001",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Resident macrophage 2",
"Sample ID":"Quigley_Inj03_SA002",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Resident macrophage 3",
"Sample ID":"Quigley_Inj09_SA003",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Resident macrophage 4",
"Sample ID":"Quigley_Inj08_SA004",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Resident macrophage 5",
"Sample ID":"Quigley_Inj11_SA005",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Resident macrophage 6",
"Sample ID":"Quigley_Inj05_SA006",
"Factors":{"Treatment":"Resident macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 1",
"Sample ID":"Quigley_Inj06_SA007",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 2",
"Sample ID":"Quigley_Inj07_SA008",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 3",
"Sample ID":"Quigley_Inj10_SA009",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 4",
"Sample ID":"Quigley_Inj13_SA010",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 5",
"Sample ID":"Quigley_Inj14_SA011",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
},
{
"Subject ID":"Bone marrow macrophage 6",
"Sample ID":"Quigley_Inj04_SA012",
"Factors":{"Treatment":"Bone marrow macrophage"},
"Additional sample data":{"Organ":"Cells","Species":"Mouse"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were centrifuged at 500g in PBS, the supernatant aspirated and the cell pellet snap frozen in liquid nitrogen","COLLECTION_PROTOCOL_FILENAME":"StudyDesign-LauraQuigley-121214.pdf","SAMPLE_TYPE":"Cell"},

"TREATMENT":{"TREATMENT_SUMMARY":"Different cell types: 1. Peritoneal macrophages 2. Bone marrow derived macrophages","TREATMENT_PROTOCOL_FILENAME":"StudyDesign-LauraQuigley-121214.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C.","SAMPLEPREP_PROTOCOL_FILENAME":"SOP_Extraction_of_Yeast_Cells.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"UPLC","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6530","COLUMN_NAME":"Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) 1.7um Pre-Column","FLOW_GRADIENT":"15% B to 99% B","FLOW_RATE":"0.6 mL/min","COLUMN_TEMPERATURE":"65 C","METHODS_FILENAME":"Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf","SOLVENT_A":"60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid","SOLVENT_B":"9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid","COLUMN_PRESSURE":"450-850 bar","INTERNAL_STANDARD":"See data dictionary","RETENTION_TIME":"See data dictionary","SAMPLE_INJECTION":"1.67 uL","ANALYTICAL_TIME":"13 min","CAPILLARY_VOLTAGE":"3500","TIME_PROGRAM":"15 min","WEAK_WASH_SOLVENT_NAME":"Isopropanol","WEAK_WASH_VOLUME":"5 seconds","STRONG_WASH_SOLVENT_NAME":"same","TARGET_SAMPLE_TEMPERATURE":"Autosampler temp 4 C","RANDOMIZATION_ORDER":"Excel"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","DETECTOR_TYPE":"TOF MCP","SOFTWARE_VERSION":"MassHunter","DATA_FORMAT":".d"},

"MS":{"INSTRUMENT_NAME":"Agilent 6530 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)","DRY_GAS_FLOW":"8 l/min","DRY_GAS_TEMP":"325","FRAGMENT_VOLTAGE":"120","FRAGMENTATION_METHOD":"Auto MS/MS","ION_SOURCE_TEMPERATURE":"325","ION_SPRAY_VOLTAGE":"1000","IONIZATION":"Pos","PRECURSOR_TYPE":"Intact Molecule","REAGENT_GAS":"Nitrogen","SOURCE_TEMPERATURE":"325","DESOLVATION_GAS_FLOW":"11 l/min","DESOLVATION_TEMPERATURE":"350","NEBULIZER":"35 psig","OCTPOLE_VOLTAGE":"750","RESOLUTION_SETTING":"Extended Dynamic Range","SCAN_RANGE_MOVERZ":"60-1700 Da","SCANNING_CYCLE":"2 Hz","SCANNING_RANGE":"60-1700 Da","SKIMMER_VOLTAGE":"65"},

"MS_METABOLITE_DATA":{
"Units":"peak height",

"Data":[{"Metabolite":"CE (18:1)","Quigley_Inj12_SA001":"","Quigley_Inj03_SA002":"","Quigley_Inj09_SA003":"","Quigley_Inj08_SA004":"","Quigley_Inj11_SA005":"","Quigley_Inj05_SA006":"","Quigley_Inj06_SA007":"6568","Quigley_Inj07_SA008":"13106","Quigley_Inj10_SA009":"7139","Quigley_Inj13_SA010":"12237","Quigley_Inj14_SA011":"5370","Quigley_Inj04_SA012":"6395"},{"Metabolite":"CE (20:4)","Quigley_Inj12_SA001":"","Quigley_Inj03_SA002":"","Quigley_Inj09_SA003":"","Quigley_Inj08_SA004":"","Quigley_Inj11_SA005":"","Quigley_Inj05_SA006":"","Quigley_Inj06_SA007":"44059","Quigley_Inj07_SA008":"53391","Quigley_Inj10_SA009":"48004","Quigley_Inj13_SA010":"48177","Quigley_Inj14_SA011":"34916","Quigley_Inj04_SA012":"41437"},{"Metabolite":"CE (22:6)","Quigley_Inj12_SA001":"","Quigley_Inj03_SA002":"","Quigley_Inj09_SA003":"","Quigley_Inj08_SA004":"","Quigley_Inj11_SA005":"","Quigley_Inj05_SA006":"","Quigley_Inj06_SA007":"","Quigley_Inj07_SA008":"4646","Quigley_Inj10_SA009":"4455","Quigley_Inj13_SA010":"4167","Quigley_Inj14_SA011":"2621","Quigley_Inj04_SA012":"3773"},{"Metabolite":"Ceramide (d18:1/23:0)","Quigley_Inj12_SA001":"2326","Quigley_Inj03_SA002":"8547","Quigley_Inj09_SA003":"2254","Quigley_Inj08_SA004":"5043","Quigley_Inj11_SA005":"2444","Quigley_Inj05_SA006":"2475","Quigley_Inj06_SA007":"","Quigley_Inj07_SA008":"6226","Quigley_Inj10_SA009":"11394","Quigley_Inj13_SA010":"4728","Quigley_Inj14_SA011":"16378","Quigley_Inj04_SA012":"11682"},{"Metabolite":"Ceramide (d40:1)","Quigley_Inj12_SA001":"3041","Quigley_Inj03_SA002":"13338","Quigley_Inj09_SA003":"2460","Quigley_Inj08_SA004":"6446","Quigley_Inj11_SA005":"2615","Quigley_Inj05_SA006":"2955","Quigley_Inj06_SA007":"36650","Quigley_Inj07_SA008":"23739","Quigley_Inj10_SA009":"44672","Quigley_Inj13_SA010":"18592","Quigley_Inj14_SA011":"56839","Quigley_Inj04_SA012":"44269"},{"Metabolite":"Ceramide (d42:1)","Quigley_Inj12_SA001":"9762","Quigley_Inj03_SA002":"40953","Quigley_Inj09_SA003":"9855","Quigley_Inj08_SA004":"21316","Quigley_Inj11_SA005":"10342","Quigley_Inj05_SA006":"3796","Quigley_Inj06_SA007":"84808","Quigley_Inj07_SA008":"45857","Quigley_Inj10_SA009":"87297","Quigley_Inj13_SA010":"35414","Quigley_Inj14_SA011":"143350","Quigley_Inj04_SA012":"92946"},{"Metabolite":"Ceramide (d42:2)","Quigley_Inj12_SA001":"45649","Quigley_Inj03_SA002":"118885","Quigley_Inj09_SA003":"46146","Quigley_Inj08_SA004":"65716","Quigley_Inj11_SA005":"47096","Quigley_Inj05_SA006":"54560","Quigley_Inj06_SA007":"119103","Quigley_Inj07_SA008":"62341","Quigley_Inj10_SA009":"122301","Quigley_Inj13_SA010":"48210","Quigley_Inj14_SA011":"137842","Quigley_Inj04_SA012":"111003"},{"Metabolite":"Cholesterol","Quigley_Inj12_SA001":"47910","Quigley_Inj03_SA002":"54762","Quigley_Inj09_SA003":"48432","Quigley_Inj08_SA004":"48829","Quigley_Inj11_SA005":"49636","Quigley_Inj05_SA006":"48690","Quigley_Inj06_SA007":"33980","Quigley_Inj07_SA008":"15584","Quigley_Inj10_SA009":"34902","Quigley_Inj13_SA010":"14446","Quigley_Inj14_SA011":"31486","Quigley_Inj04_SA012":"33759"},{"Metabolite":"Gal-Gal-Cer(d18:1/16:0) or 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(d42:1)","Quigley_Inj12_SA001":"10748","Quigley_Inj03_SA002":"57687","Quigley_Inj09_SA003":"10320","Quigley_Inj08_SA004":"25872","Quigley_Inj11_SA005":"11218","Quigley_Inj05_SA006":"13578","Quigley_Inj06_SA007":"62538","Quigley_Inj07_SA008":"37442","Quigley_Inj10_SA009":"68441","Quigley_Inj13_SA010":"28320","Quigley_Inj14_SA011":"122341","Quigley_Inj04_SA012":"72515"},{"Metabolite":"GlcCer (d42:2)","Quigley_Inj12_SA001":"18141","Quigley_Inj03_SA002":"68829","Quigley_Inj09_SA003":"16166","Quigley_Inj08_SA004":"29070","Quigley_Inj11_SA005":"17830","Quigley_Inj05_SA006":"19787","Quigley_Inj06_SA007":"24754","Quigley_Inj07_SA008":"12485","Quigley_Inj10_SA009":"24031","Quigley_Inj13_SA010":"10868","Quigley_Inj14_SA011":"32105","Quigley_Inj04_SA012":"24291"},{"Metabolite":"LPC (16:0)","Quigley_Inj12_SA001":"35300","Quigley_Inj03_SA002":"38408","Quigley_Inj09_SA003":"27223","Quigley_Inj08_SA004":"31905","Quigley_Inj11_SA005":"35880","Quigley_Inj05_SA006":"37366","Quigley_Inj06_SA007":"11137","Quigley_Inj07_SA008":"5531","Quigley_Inj10_SA009":"11907","Quigley_Inj13_SA010":"4352","Quigley_Inj14_SA011":"8893","Quigley_Inj04_SA012":"9588"},{"Metabolite":"LPC (18:0)","Quigley_Inj12_SA001":"45015","Quigley_Inj03_SA002":"51751","Quigley_Inj09_SA003":"38541","Quigley_Inj08_SA004":"39645","Quigley_Inj11_SA005":"45139","Quigley_Inj05_SA006":"45945","Quigley_Inj06_SA007":"12592","Quigley_Inj07_SA008":"6389","Quigley_Inj10_SA009":"12674","Quigley_Inj13_SA010":"5309","Quigley_Inj14_SA011":"10385","Quigley_Inj04_SA012":"11045"},{"Metabolite":"LPC (18:1)","Quigley_Inj12_SA001":"3120","Quigley_Inj03_SA002":"3215","Quigley_Inj09_SA003":"2488","Quigley_Inj08_SA004":"2847","Quigley_Inj11_SA005":"3053","Quigley_Inj05_SA006":"3699","Quigley_Inj06_SA007":"2156","Quigley_Inj07_SA008":"1201","Quigley_Inj10_SA009":"2169","Quigley_Inj13_SA010":"864","Quigley_Inj14_SA011":"1779","Quigley_Inj04_SA012":"1957"},{"Metabolite":"PC (28:0)","Quigley_Inj12_SA001":"","Quigley_Inj03_SA002":"","Quigley_Inj09_SA003":"","Quigley_Inj08_SA004":"","Quigley_Inj11_SA005":"","Quigley_Inj05_SA006":"","Quigley_Inj06_SA007":"10537","Quigley_Inj07_SA008":"4625","Quigley_Inj10_SA009":"9131","Quigley_Inj13_SA010":"3869","Quigley_Inj14_SA011":"7130","Quigley_Inj04_SA012":"8333"},{"Metabolite":"PC (30:0)","Quigley_Inj12_SA001":"157699","Quigley_Inj03_SA002":"188921","Quigley_Inj09_SA003":"130300","Quigley_Inj08_SA004":"127718","Quigley_Inj11_SA005":"150188","Quigley_Inj05_SA006":"161562","Quigley_Inj06_SA007":"867421","Quigley_Inj07_SA008":"406537","Quigley_Inj10_SA009":"777161","Quigley_Inj13_SA010":"333011","Quigley_Inj14_SA011":"611210","Quigley_Inj04_SA012":"736542"},{"Metabolite":"PC (30:1)","Quigley_Inj12_SA001":"","Quigley_Inj03_SA002":"","Quigley_Inj09_SA003":"","Quigley_Inj08_SA004":"","Quigley_Inj11_SA005":"","Quigley_Inj05_SA006":"","Quigley_Inj06_SA007":"11390","Quigley_Inj07_SA008":"5604","Quigley_Inj10_SA009":"10164","Quigley_Inj13_SA010":"4109","Quigley_Inj14_SA011":"8161","Quigley_Inj04_SA012":"9245"},{"Metabolite":"PC 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(32:1)","Quigley_Inj12_SA001":"125337","Quigley_Inj03_SA002":"145986","Quigley_Inj09_SA003":"101971","Quigley_Inj08_SA004":"97888","Quigley_Inj11_SA005":"110956","Quigley_Inj05_SA006":"124080","Quigley_Inj06_SA007":"392554","Quigley_Inj07_SA008":"183548","Quigley_Inj10_SA009":"345702","Quigley_Inj13_SA010":"150472","Quigley_Inj14_SA011":"274513","Quigley_Inj04_SA012":"333649"},{"Metabolite":"PC (33:0)","Quigley_Inj12_SA001":"21775","Quigley_Inj03_SA002":"28437","Quigley_Inj09_SA003":"20008","Quigley_Inj08_SA004":"20487","Quigley_Inj11_SA005":"22555","Quigley_Inj05_SA006":"24208","Quigley_Inj06_SA007":"127655","Quigley_Inj07_SA008":"64273","Quigley_Inj10_SA009":"112271","Quigley_Inj13_SA010":"51218","Quigley_Inj14_SA011":"86510","Quigley_Inj04_SA012":"106501"},{"Metabolite":"PC (33:1)","Quigley_Inj12_SA001":"11571","Quigley_Inj03_SA002":"14004","Quigley_Inj09_SA003":"10501","Quigley_Inj08_SA004":"10263","Quigley_Inj11_SA005":"11538","Quigley_Inj05_SA006":"11503","Quigley_Inj06_SA007":"130703","Quigley_Inj07_SA008":"63492","Quigley_Inj10_SA009":"111062","Quigley_Inj13_SA010":"52494","Quigley_Inj14_SA011":"91476","Quigley_Inj04_SA012":"110918"},{"Metabolite":"PC (34:0)","Quigley_Inj12_SA001":"261173","Quigley_Inj03_SA002":"349513","Quigley_Inj09_SA003":"232228","Quigley_Inj08_SA004":"224821","Quigley_Inj11_SA005":"270300","Quigley_Inj05_SA006":"286561","Quigley_Inj06_SA007":"1108096","Quigley_Inj07_SA008":"554985","Quigley_Inj10_SA009":"1018357","Quigley_Inj13_SA010":"449974","Quigley_Inj14_SA011":"802996","Quigley_Inj04_SA012":"944057"},{"Metabolite":"PC (34:1)","Quigley_Inj12_SA001":"1257177","Quigley_Inj03_SA002":"1466862","Quigley_Inj09_SA003":"1117567","Quigley_Inj08_SA004":"1075363","Quigley_Inj11_SA005":"1257773","Quigley_Inj05_SA006":"1359932","Quigley_Inj06_SA007":"2617784","Quigley_Inj07_SA008":"1207315","Quigley_Inj10_SA009":"2351998","Quigley_Inj13_SA010":"1022913","Quigley_Inj14_SA011":"1953824","Quigley_Inj04_SA012":"2260384"},{"Metabolite":"PC (34:2)","Quigley_Inj12_SA001":"920491","Quigley_Inj03_SA002":"1087525","Quigley_Inj09_SA003":"843918","Quigley_Inj08_SA004":"797640","Quigley_Inj11_SA005":"977492","Quigley_Inj05_SA006":"1031498","Quigley_Inj06_SA007":"338773","Quigley_Inj07_SA008":"160536","Quigley_Inj10_SA009":"296691","Quigley_Inj13_SA010":"133273","Quigley_Inj14_SA011":"240753","Quigley_Inj04_SA012":"284391"},{"Metabolite":"PC 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