{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000241","ANALYSIS_ID":"AN000373","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical of structure and function in HepG2 cells","PROJECT_TYPE":"Lipidomics","PROJECT_SUMMARY":"Five analogues of OA (18:1cis9) or elaidic acid (18:1trans9) replacing the with a four-membered carbocycle were evaluated in HepG2 cells, which are models for hepatocytes. In order to assess whether or not the novel analogues incorporated into complex lipids, cells were treated with compond and then extracted. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry was employed for the analysis of complex lipids. Data processing involved mass chromatographic peak detection and deconvolution, isotopic peaks grouping, and peak alignment. Significantly altered metabolites were defined by a fold (FC) >2 and p<0.05. Principal component analysis (PCA) and hierarchical analysis (HCA) of signature metabolites altered in compounds treated cells to control were performed in the Metaboanalyst web portal","INSTITUTE":"University of Nebraska-Lincoln","DEPARTMENT":"Biochemistry","LABORATORY":"DiRusso Black FATTT Lab","LAST_NAME":"DiRusso","FIRST_NAME":"Concetta","ADDRESS":"Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center Vine St.","EMAIL":"cdirusso2@unl.edu","PHONE":"402-472-6504 or 402-613-9293","FUNDING_SOURCE":"NIH"},

"STUDY":{"STUDY_TITLE":"Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical of structure and function in HepG2 cells","STUDY_TYPE":"Lipid analysis novel C18 fatty acid anologues in complex lipids","STUDY_SUMMARY":"Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. treatment with fatty acids or analogues, the cells were seeded at a density of × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to the desired final concentration. The controls in these experiments were HepG2 with BSA alone. After 24 h treatment, the media was collected, cells were twice with PBS and cells were harvested for analysis. To each cell suspension to lipid extraction a standard mixture of 25 µg C15:0 PE, C17:0 PC and C71:1 was added as standards. Extraction of lipids was performed according to the method. For metabolomics analysis, the lipid extracts were resuspended in 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), The injection volume was 4 µL. Separation of metabolites was achieved at the gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar software. MS data was collected with resolving power of 78,000 (at m/z 400) in or negative mode under following conditions: a capillary voltage of (+/-) 4,500 and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing mass detection, chromatographic peak detection and deconvolution, isotopic grouping, normalization and peak alignment. Metabolite data were mean-centered unit-variance scaled to remove the offsets and adjust the importance of high low abundance metabolites to an equal level. Significantly altered metabolites defined by a fold change (FC) >2 and p<0.05. Principal component analysis (PCA) hierarchical clustering analysis (HCA) of signature metabolites altered in treated cells compared to control were performed in the Metaboanalyst web (www.metaboanalyst.ca).","INSTITUTE":"University of Nebraska - Lincoln","DEPARTMENT":"Biochemistry","LABORATORY":"DiRusso Black FATTT Lab","LAST_NAME":"DiRusso","FIRST_NAME":"Concetta","ADDRESS":"Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center Vine St.","EMAIL":"cdirusso2@unl.edu","PHONE":"402-472-6504 or 402-613-9293","NUM_GROUPS":"8","TOTAL_SUBJECTS":"24+24=48","STUDY_COMMENTS":"8 groups in triplicate ran in both negative and positive mode"},

"SUBJECT":{"SUBJECT_TYPE":"Human cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","CELL_BIOSOURCE_OR_SUPPLIER":"ATCC","CELL_STRAIN_DETAILS":"HepG2","SUBJECT_COMMENTS":"NA","CELL_PRIMARY_IMMORTALIZED":"Immortalized","CELL_PASSAGE_NUMBER":"NA","CELL_COUNTS":"NA"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Control1",
"Factors":{"Concentration (uM)":"0","Treatment_compound":"BSA"},
"Additional sample data":{"Sample_Data":"BSA"}
},
{
"Subject ID":"-",
"Sample ID":"Control2",
"Factors":{"Concentration (uM)":"0","Treatment_compound":"BSA"},
"Additional sample data":{"Sample_Data":"BSA"}
},
{
"Subject ID":"-",
"Sample ID":"Control3",
"Factors":{"Concentration (uM)":"0","Treatment_compound":"BSA"},
"Additional sample data":{"Sample_Data":"BSA"}
},
{
"Subject ID":"-",
"Sample ID":"FAC1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-cis"},
"Additional sample data":{"Sample_Data":"CB-cis, cis (1S*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"FAC2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-cis"},
"Additional sample data":{"Sample_Data":"CB-cis, cis (1S*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"FAC3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-cis"},
"Additional sample data":{"Sample_Data":"CB-cis, cis (1S*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"FAT1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-trans"},
"Additional sample data":{"Sample_Data":"CB-trans, trans (1R*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"FAT2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-trans"},
"Additional sample data":{"Sample_Data":"CB-trans, trans (1R*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"FAT3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CB-trans"},
"Additional sample data":{"Sample_Data":"CB-trans, trans (1R*,4R*)-4-octyl-2-cyclobutene-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKC1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-cis"},
"Additional sample data":{"Sample_Data":"CK-cis, (1S*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKC2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-cis"},
"Additional sample data":{"Sample_Data":"CK-cis, (1S*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKC3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-cis"},
"Additional sample data":{"Sample_Data":"CK-cis, (1S*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKT1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-trans"},
"Additional sample data":{"Sample_Data":"CK-trans, (1R*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKT2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-trans"},
"Additional sample data":{"Sample_Data":"CK-trans, (1R*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"CKT3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"CK-trans"},
"Additional sample data":{"Sample_Data":"CK-trans, (1R*,3RS,4R*)-3-chloro-4-octyl-2-oxo cyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"KC1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"K-cis"},
"Additional sample data":{"Sample_Data":"K-cis, cis-(1S*,4R*)- 4-octyl-2-oxocyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"KC2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"K-cis"},
"Additional sample data":{"Sample_Data":"K-cis, cis-(1S*,4R*)- 4-octyl-2-oxocyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"KC3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"K-cis"},
"Additional sample data":{"Sample_Data":"K-cis, cis-(1S*,4R*)- 4-octyl-2-oxocyclobutane-1-octanoic acid"}
},
{
"Subject ID":"-",
"Sample ID":"OA1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Oleic acid"},
"Additional sample data":{"Sample_Data":"Oleic acid"}
},
{
"Subject ID":"-",
"Sample ID":"OA2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Oleic acid"},
"Additional sample data":{"Sample_Data":"Oleic acid"}
},
{
"Subject ID":"-",
"Sample ID":"OA3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Oleic acid"},
"Additional sample data":{"Sample_Data":"Oleic acid"}
},
{
"Subject ID":"-",
"Sample ID":"PA1",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Palmitic acid"},
"Additional sample data":{"Sample_Data":"Palmitic acid"}
},
{
"Subject ID":"-",
"Sample ID":"PA2",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Palmitic acid"},
"Additional sample data":{"Sample_Data":"Palmitic acid"}
},
{
"Subject ID":"-",
"Sample ID":"PA3",
"Factors":{"Concentration (uM)":"500","Treatment_compound":"Palmitic acid"},
"Additional sample data":{"Sample_Data":"Palmitic acid"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells treated 24hr with 500 µM Fa, analogue or BSA control. Harvested and extracted and then resolved using Fourier Transform Ion Cyclotron Resonance Spectrometry (FTICR-MS) s","TREATMENT_PROTOCOL_ID":"CBC_treatment","TREATMENT_PROTOCOL_FILENAME":"See_Comments","TREATMENT_PROTOCOL_COMMENTS":"Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. treatment with fatty acids or analogues, the cells were seeded at a density of × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to 500µM final concentration. The controls in these experiments were HepG2 cells BSA alone. After 24 h treatment, the media was collected, cells were rinsed with PBS and cells were harvested for complex lipid analysis.","TREATMENT_COMPOUND":"Fatty acid/BSA","TREATMENT_DOSE":"500 µM (fatty acid)","TREATMENT_DOSEDURATION":"24 hr","TREATMENT_VEHICLE":"PBS","CELL_GROWTH_CONTAINER":"75 ml tissue cell culture flasks","CELL_MEDIA":"Eagle's minimal essential medium (EMEM) augmented with 10% fetal bovine serum","CELL_ENVIR_COND":"37°C in a humidified atmosphere with 5% CO2","CELL_HARVESTING":"Typsinize and scrape","CELL_MEDIA_LASTCHANGED":"24 hr"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_COMMENTS":"For metabolomics analysis, the lipid extracts were resuspended in 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), The injection volume was 4 µL. Separation of metabolites was achieved at the gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar software. MS data was collected with resolving power of 78,000 (at m/z 400) in or negative mode under following conditions: a capillary voltage of (+/-) 4,500 and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing mass detection, chromatographic peak detection and deconvolution, isotopic grouping, normalization and peak alignment.","EXTRACTION_METHOD":"Folche Lipid Extraction: Folch J, Lees M, Sloane-Stanley GH. A simple method the isolation and purification of total lipids from animal tissues. J biol 1957;226:497-509.","SAMPLE_SPIKING":"25 µg C15:0 PE, C17:0 PC and C71:1 TAG added to 2 X 10e6 cells prior to lipid","CELL_TYPE":"HepG2"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1200","COLUMN_NAME":"ACE 5 C8-300 (100 x 2.1mm)","METHODS_FILENAME":"jac8lipidneg.m","CHROMATOGRAPHY_COMMENTS":"jalcms1lipneg.m","FLOW_RATE":"0.1 mL/min","INTERNAL_STANDARD":"25 g C15:0 PE, C17:0 PC and C71:1 TAG","SOLVENT_A":"0.1% formic acid; 10 mM ammonium acetate in H2O","SOLVENT_B":"0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v)","ANALYTICAL_TIME":"60 min"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"DiRusso Black FATTT Lab","SOFTWARE_VERSION":"Compass solariXcontrol v1.5.0 103 (February 28, 2011)","DETECTOR_TYPE":"msDetector","DATA_FORMAT":"*.baf"},

"MS":{"INSTRUMENT_NAME":"Bruker SolariX FT-ICR-MS","INSTRUMENT_TYPE":"FT-ICR-MS","MS_TYPE":"ESI","ION_MODE":"POSITIVE","DATAFORMAT":"*.d","MS_COMMENTS":"Results for unique + mode identifications with each fatty acid are available 3)-O-b-D-galactopyranosyl-(1->4)-O-2-(acetylamino)-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)-O-2-(acetylamino)-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)- D-Gluc","Control1":"82600000.0000","Control2":"71400000.0000","Control3":"66400000.0000","FAC1":"39300000.0000","FAC2":"42000000.0000","FAC3":"41100000.0000","FAT1":"46600000.0000","FAT2":"44400000.0000","FAT3":"42900000.0000","CKC1":"69200000.0000","CKC2":"65000000.0000","CKC3":"62400000.0000","CKT1":"56000000.0000","CKT2":"50700000.0000","CKT3":"60100000.0000","KC1":"60400000.0000","KC2":"54100000.0000","KC3":"55900000.0000","OA1":"42000000.0000","OA2":"35500000.0000","OA3":"35900000.0000","PA1":"38300000.0000","PA2":"37400000.0000","PA3":"34500000.0000"},{"Metabolite":"P1_P4-Bis(5^-adenosyl) tetraphosphate","Control1":"","Control2":"","Control3":"","FAC1":"","FAC2":"","FAC3":"","FAT1":"","FAT2":"","FAT3":"","CKC1":"11300000.0000","CKC2":"374000.0000","CKC3":"2820000.0000","CKT1":"","CKT2":"","CKT3":"","KC1":"","KC2":"404000.0000","KC3":"","OA1":"","OA2":"409000.0000","OA3":"","PA1":"","PA2":"","PA3":""},{"Metabolite":"Palmitic 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}

}