{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000084","ANALYSIS_ID":"AN000136","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Systems Biology for EnteroPathogens","PROJECT_TYPE":"MS analysis","PROJECT_SUMMARY":"sysbep.org","INSTITUTE":"Pacific Northwest National Laboratory","DEPARTMENT":"Biological Separation and Mass Spectrometry","LAST_NAME":"Joshua","FIRST_NAME":"Adkins","ADDRESS":"-","EMAIL":"Joshua.Adkins@pnnl.gov","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Model-driven multi-omic data analysis elucidates metabolic immunomodulators of activation","STUDY_TYPE":"growth condition, timecourse","STUDY_SUMMARY":"Macrophages are central players in immune response, manifesting divergent to control inflammation and innate immunity through release of cytokines and signaling factors. Recently, the focus on metabolism has been reemphasized as signaling and regulatory pathways of human pathophysiology, ranging from cancer aging, often converge on metabolic responses. Here, we used genome-scale and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to metabolic features that are critical for macrophage activation. A genome-scale network for the RAW 264.7 cell line was constructed to determine metabolic of activation. Metabolites well-known to be associated with immunoactivation and arginine) and immunosuppression (tryptophan and vitamin D3) were among the critical effectors. Intracellular metabolic mechanisms were assessed, a suppressive role for de-novo nucleotide synthesis. Finally, underlying mechanisms of macrophage activation were identified by analyzing multi-omic obtained from LPS-stimulated RAW cells in the context of our flux-based This study demonstrates that the role of metabolism in regulating activation be greater than previously anticipated and elucidates underlying connections activation and metabolic effectors. This submission corresponds to the data from this study.","INSTITUTE":"Pacific Northwest National Laboratory","DEPARTMENT":"Biological Separation and Mass Spectrometry","LAST_NAME":"Metz","FIRST_NAME":"Thomas","ADDRESS":"-","EMAIL":"thomas.metz@pnnl.gov","PHONE":"-","NUM_GROUPS":"2","TOTAL_SUBJECTS":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"RAW 264.7","CELL_STRAIN_DETAILS":"RAW 264.7","CELL_PRIMARY_IMMORTALIZED":"immortalized","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_LPSactivated1",
"Factors":{"Lipopolysaccharide Treatment":"100 ng/ml"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_LPSactivated2",
"Factors":{"Lipopolysaccharide Treatment":"100 ng/ml"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_LPSactivated3",
"Factors":{"Lipopolysaccharide Treatment":"100 ng/ml"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_Control1",
"Factors":{"Lipopolysaccharide Treatment":"None"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_Control2",
"Factors":{"Lipopolysaccharide Treatment":"None"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Metab_Control3",
"Factors":{"Lipopolysaccharide Treatment":"None"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After stimulation, cells were washed twice with Dulbecco?s PBS, scraped out and into 15-mL centrifuge tubes.","SAMPLE_TYPE":"Cell","COLLECTION_METHOD":"After stimulation, cells were washed twice with Dulbecco?s PBS, scraped out and into 15-mL centrifuge tubes.","COLLECTION_TIME":"24 hours","COLLECTION_VIALS":"15-mL centrifuge tubes","TISSUE_CELL_QUANTITY_TAKEN":"All"},

"TREATMENT":{"TREATMENT_SUMMARY":"Macrophages (RAW 264.7 cells) grown for two day with suplimentation of 100ng | lipopolysaccharide | Macrophages (RAW 264.7 cells) grown for two days without","TREATMENT_PROTOCOL_COMMENTS":"Macrophages (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm using Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf then grown for 2 days and stimulated for 24 hours with 100 ng/mL of diluted in fresh medium. A control culture was run in parallel by incubating the same period of time with fresh medium only. Three biological replicates performed per condition, and two dishes were used for each replicate. / (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm dishes Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf serum, then for 2 days and stimulated for 24 hours with 100 ng/mL of lipopolysaccharide in fresh medium. A control culture was run in parallel by incubating for the period of time with fresh medium only. Three biological replicates were per condition, and two dishes were used for each replicate.","TREATMENT":"Abiotic","TREATMENT_COMPOUND":"lipopolysaccharide / fresh medium","TREATMENT_DOSE":"100 ng/mL /--","TREATMENT_VEHICLE":"fresh medium","CELL_GROWTH_CONTAINER":"150 mm dishes","CELL_INOC_PROC":"Macrophages (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm","CELL_MEDIA":"Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf serum","CELL_HARVESTING":"After stimulation, cells were washed twice with Dulbecco?s PBS, scraped out and into 15-mL centrifuge tubes."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Suspentions softly centrifuged, buffer removed, amonium bicarbonate added, extraxted with chloroform/methanol (2:1, v/v), vortexed, centrifuged, aqueous dried in vacuum concentrator, derivatization with methoxyamine in pyridine, (MSTFA), and 1% trimethylchlorosilane (TMCS)","SAMPLEPREP_PROTOCOL_COMMENTS":"Cell suspensions were softly centrifuged (230 × g for 5 min) and as much as possible was removed. Then, 170 µL of 150 mM ammonium bicarbonate was added the cell pellet and the cell suspensions were transferred to 2 mL tubes for extraction. Subsequently, the water soluble metabolites were with four volumes of chilled (-20°C) chloroform/methanol (2:1, v/v). After the samples were centrifuged (12,000 × g for 5 min) and the upper (aqueous) containing water-soluble metabolites were transferred into glass vials, by drying in a vacuum concentrator. For the derivatization, 20 µL of in pyridine (30 mg/mL) were added to each sample, followed by incubation at with shaking for 90 min to protect carbonyl groups. Next, 80 µL of (MSTFA) with 1% trimethylchlorosilane (TMCS) were added to each vial, followed incubation at 37°C with shaking for 30 min to derivatize hydroxyl and amine The samples were then allowed to cool to room temperature.","PROCESSING_METHOD":"Homogenization","EXTRACTION_METHOD":"The water soluble metabolites were extracted with four volumes of chilled chloroform/methanol (2:1, v/v). After vortexing, the samples were centrifuged × g for 5 min) and the upper (aqueous) layers containing water-soluble were transferred into glass vials, followed by drying in a vacuum concentrator.","EXTRACT_ENRICHMENT":"Vacuum Concentrator","SAMPLE_RESUSPENSION":"20 µL of methoxyamine in pyridine (30 mg/mL)","SAMPLE_DERIVATIZATION":"20 µL of methoxyamine in pyridine (30 mg/mL), 80 µL of (MSTFA) with 1% trimethylchlorosilane (TMCS),","CELL_TYPE":"Macrophage"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Agilent 7890A gas chromatograph with a HP-5MS gas chromatography column using","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Agilent HP5-MS (30m × 0.25mm, 0.25 um)","CHROMATOGRAPHY_COMMENTS":"Chromatography was carried out on an Agilent 7890A gas chromatograph using the software (Chemstation) and a HP-5MS gas chromatography column (Agilent Santa Clara, CA; 30 m x 0.25 mm x 0.25 m film thickness). The sample injection was splitless, and 1 L of each sample was injected. The injection port was held at 250 C throughout the analysis. The GC oven was held at 60 C for 1 after injection, and the temperature was then increased to 325 C by 10 C/min, by a 5 min hold at 325 C. The helium gas flow rates for each Experiment were by the Agilent Retention Time Locking function based on analysis of deuterated acid and were in the range of 0.450.5 mL/min.","FLOW_RATE":"0.45-0.5mL/min","INJECTION_TEMPERATURE":"250 C","SAMPLE_INJECTION":"1 L, Splitless","ANALYTICAL_TIME":"37.5 min","OVEN_TEMPERATURE":"60 C for 1 min, then increased to 325 C by 10 C/min, followed by a 5 min hold 325 C","SAMPLE_SYRINGE_SIZE":"10 L"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Biological Separations & Mass Spectrometry group, Pacific Northwest National (www.omics.pnl.gov)","ACQUISITION_DATE":"2012","SOFTWARE_VERSION":"Metabolite Detector vs. 2.0.6 beta","DATA_FORMAT":"Raw .D.Zip; Processed .CDF"},

"MS":{"INSTRUMENT_NAME":"Agilent 5975C","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"After converting raw data to netCDF format, the data were processed by the software for peak deconvolution and chromatographic alignment. Retention (RI) were calculated based on the analysis of a mixture of fatty acid methyl (C8 - C30) (Agilent Technologies) as external retention time standards, then retention index information was subsequently applied to all experimental for retention time alignment. MetaboliteDetector parameters for peak detection deconvolution are as follows: Peak threshold, 7; minimum peak height, 7; width, 8. Deconvoluted features were identified by matching to the Agilent Metabolomics Retention Time Locked Library, which contains mass spectral and indix information for approximately 700 metabolites. Each initial match to the was manually inspected to confirm a confident identification. The data were matched against the NIST 08 library to identify additional peaks not included the Fiehn library. MetaboliteDetector software was used for database matching batch identification/quantification parameters are as follows: required score, ?RI, 25; minimum S/N, 20; maximum peak discrepancy index, 100. Ions 73 and 143 excluded from use as metabolite quantification ions, since these are due to of the trimethylsilyl groups. Otherwise, three unique fragment ions were to each metabolite for quantification and used for each individual GC-MS when processing the data in batch mode. The summed areas of the three ions were exported from MetaboliteDetector and used in further statistical All identifications were manually validated by inspection of retention index spectrum matches.","SCAN_RANGE_MOVERZ":"50-550 m/z"},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"1-methyl nicotinamide","SBEP_Metab_LPSactivated1":"1128844.9000","SBEP_Metab_LPSactivated2":"990557.0975","SBEP_Metab_LPSactivated3":"1142586.6960","SBEP_Metab_Control1":"1117011.1816","SBEP_Metab_Control2":"1315764.9690","SBEP_Metab_Control3":"1609434.2165"},{"Metabolite":"2-aminoethanethiol","SBEP_Metab_LPSactivated1":"941833.5000","SBEP_Metab_LPSactivated2":"868973.5000","SBEP_Metab_LPSactivated3":"953831.6860","SBEP_Metab_Control1":"1600093.6015","SBEP_Metab_Control2":"1964054.9380","SBEP_Metab_Control3":"2213228.8040"},{"Metabolite":"3-hydroxybenzaldehyde","SBEP_Metab_LPSactivated1":"501242.7073","SBEP_Metab_LPSactivated2":"431011.4386","SBEP_Metab_LPSactivated3":"477214.9231","SBEP_Metab_Control1":"","SBEP_Metab_Control2":"","SBEP_Metab_Control3":""},{"Metabolite":"3-phosphoglyceric acid","SBEP_Metab_LPSactivated1":"1303610.3515","SBEP_Metab_LPSactivated2":"1504818.0300","SBEP_Metab_LPSactivated3":"1740486.5540","SBEP_Metab_Control1":"877204.8435","SBEP_Metab_Control2":"1211525.0710","SBEP_Metab_Control3":"1272797.0990"},{"Metabolite":"4-guanidinobutyric acid","SBEP_Metab_LPSactivated1":"1859373.2670","SBEP_Metab_LPSactivated2":"1685591.6650","SBEP_Metab_LPSactivated3":"1858273.8870","SBEP_Metab_Control1":"2645271.9460","SBEP_Metab_Control2":"2600277.8205","SBEP_Metab_Control3":"3854828.0225"},{"Metabolite":"4-hydroxyquinoline-2-carboxylic acid","SBEP_Metab_LPSactivated1":"177836.4865","SBEP_Metab_LPSactivated2":"168974.9107","SBEP_Metab_LPSactivated3":"193569.5687","SBEP_Metab_Control1":"2110118.1290","SBEP_Metab_Control2":"2221603.0990","SBEP_Metab_Control3":"2535250.0470"},{"Metabolite":"5^-deoxy-5^-(methylthio)adenosine","SBEP_Metab_LPSactivated1":"2882511.8800","SBEP_Metab_LPSactivated2":"2957775.4975","SBEP_Metab_LPSactivated3":"2724568.3550","SBEP_Metab_Control1":"464864.2507","SBEP_Metab_Control2":"589460.9126","SBEP_Metab_Control3":"780203.1709"},{"Metabolite":"adenosine","SBEP_Metab_LPSactivated1":"1537097.8750","SBEP_Metab_LPSactivated2":"1214250.8015","SBEP_Metab_LPSactivated3":"1316169.5090","SBEP_Metab_Control1":"4053242.8525","SBEP_Metab_Control2":"4148655.7665","SBEP_Metab_Control3":"4784051.0780"},{"Metabolite":"adenosine-5-monophosphate","SBEP_Metab_LPSactivated1":"9454142.7335","SBEP_Metab_LPSactivated2":"8121689.6410","SBEP_Metab_LPSactivated3":"8463618.3950","SBEP_Metab_Control1":"27543792.1050","SBEP_Metab_Control2":"34940220.5400","SBEP_Metab_Control3":"42146640.0400"},{"Metabolite":"alpha ketoglutaric acid","SBEP_Metab_LPSactivated1":"","SBEP_Metab_LPSactivated2":"","SBEP_Metab_LPSactivated3":"","SBEP_Metab_Control1":"2092664.4335","SBEP_Metab_Control2":"2059916.6520","SBEP_Metab_Control3":"2437121.8085"},{"Metabolite":"arabitol","SBEP_Metab_LPSactivated1":"390153.2435","SBEP_Metab_LPSactivated2":"387118.4070","SBEP_Metab_LPSactivated3":"454665.9208","SBEP_Metab_Control1":"","SBEP_Metab_Control2":"","SBEP_Metab_Control3":""},{"Metabolite":"beta- alanine","SBEP_Metab_LPSactivated1":"12036820.1650","SBEP_Metab_LPSactivated2":"10851261.8450","SBEP_Metab_LPSactivated3":"13599141.0650","SBEP_Metab_Control1":"23432641.8050","SBEP_Metab_Control2":"24002849.8650","SBEP_Metab_Control3":"30832474.5100"},{"Metabolite":"citraconic acid","SBEP_Metab_LPSactivated1":"6589380.9000","SBEP_Metab_LPSactivated2":"6127515.1420","SBEP_Metab_LPSactivated3":"7514006.2660","SBEP_Metab_Control1":"","SBEP_Metab_Control2":"","SBEP_Metab_Control3":""},{"Metabolite":"citric acid","SBEP_Metab_LPSactivated1":"682651.2431","SBEP_Metab_LPSactivated2":"498260.2384","SBEP_Metab_LPSactivated3":"538841.7364","SBEP_Metab_Control1":"1070709.0001","SBEP_Metab_Control2":"948590.2074","SBEP_Metab_Control3":"1063573.1426"},{"Metabolite":"creatinine","SBEP_Metab_LPSactivated1":"10452669.1560","SBEP_Metab_LPSactivated2":"10339577.5660","SBEP_Metab_LPSactivated3":"11304334.0600","SBEP_Metab_Control1":"14319437.0950","SBEP_Metab_Control2":"12841146.2800","SBEP_Metab_Control3":"16519702.7700"},{"Metabolite":"Cysteinylglycine","SBEP_Metab_LPSactivated1":"","SBEP_Metab_LPSactivated2":"","SBEP_Metab_LPSactivated3":"","SBEP_Metab_Control1":"747331.7561","SBEP_Metab_Control2":"634460.2773","SBEP_Metab_Control3":"848180.1665"},{"Metabolite":"D-galactose","SBEP_Metab_LPSactivated1":"","SBEP_Metab_LPSactivated2":"","SBEP_Metab_LPSactivated3":"","SBEP_Metab_Control1":"523849.8309","SBEP_Metab_Control2":"545109.2323","SBEP_Metab_Control3":"811281.7084"},{"Metabolite":"D-glucosaminic acid","SBEP_Metab_LPSactivated1":"26639733.4550","SBEP_Metab_LPSactivated2":"28680203.6300","SBEP_Metab_LPSactivated3":"29834683.9500","SBEP_Metab_Control1":"1869625.0015","SBEP_Metab_Control2":"2704562.6160","SBEP_Metab_Control3":"3391397.5005"},{"Metabolite":"D-glucose-6-phosphate","SBEP_Metab_LPSactivated1":"1721774.7810","SBEP_Metab_LPSactivated2":"1643900.4280","SBEP_Metab_LPSactivated3":"1763549.7790","SBEP_Metab_Control1":"","SBEP_Metab_Control2":"","SBEP_Metab_Control3":""},{"Metabolite":"DL-3-aminoisobutyric acid","SBEP_Metab_LPSactivated1":"172434.6981","SBEP_Metab_LPSactivated2":"92082.6045","SBEP_Metab_LPSactivated3":"141553.3294","SBEP_Metab_Control1":"1511728.4585","SBEP_Metab_Control2":"1461268.2315","SBEP_Metab_Control3":"2514955.0150"},{"Metabolite":"DL-threo-beta-Hydroxyaspartic acid","SBEP_Metab_LPSactivated1":"95146.8605","SBEP_Metab_LPSactivated2":"103992.0491","SBEP_Metab_LPSactivated3":"120882.9009","SBEP_Metab_Control1":"170726.0954","SBEP_Metab_Control2":"335916.9590","SBEP_Metab_Control3":"425773.9757"},{"Metabolite":"D-malic acid","SBEP_Metab_LPSactivated1":"1147617.8690","SBEP_Metab_LPSactivated2":"1135687.1810","SBEP_Metab_LPSactivated3":"1415029.3205","SBEP_Metab_Control1":"4107528.9195","SBEP_Metab_Control2":"3486786.6035","SBEP_Metab_Control3":"4118208.6520"},{"Metabolite":"D-mannitol","SBEP_Metab_LPSactivated1":"2946232.9380","SBEP_Metab_LPSactivated2":"2897797.4370","SBEP_Metab_LPSactivated3":"3412819.1040","SBEP_Metab_Control1":"1900178.9300","SBEP_Metab_Control2":"1597070.3660","SBEP_Metab_Control3":"1223019.2760"},{"Metabolite":"D-Ribose 5-phosphate","SBEP_Metab_LPSactivated1":"2229996.4555","SBEP_Metab_LPSactivated2":"2427192.3445","SBEP_Metab_LPSactivated3":"2573543.4410","SBEP_Metab_Control1":"3592947.2585","SBEP_Metab_Control2":"5229012.1725","SBEP_Metab_Control3":"8143540.4925"},{"Metabolite":"D-sorbitol","SBEP_Metab_LPSactivated1":"589958.5707","SBEP_Metab_LPSactivated2":"435463.2498","SBEP_Metab_LPSactivated3":"518026.4727","SBEP_Metab_Control1":"249105.8004","SBEP_Metab_Control2":"207333.6954","SBEP_Metab_Control3":"190275.6371"},{"Metabolite":"D-threitol","SBEP_Metab_LPSactivated1":"1081927.9775","SBEP_Metab_LPSactivated2":"1084599.8660","SBEP_Metab_LPSactivated3":"1233440.0695","SBEP_Metab_Control1":"1162887.3080","SBEP_Metab_Control2":"1628252.2225","SBEP_Metab_Control3":"1772900.8970"},{"Metabolite":"fructose","SBEP_Metab_LPSactivated1":"2037004.2305","SBEP_Metab_LPSactivated2":"2114549.7710","SBEP_Metab_LPSactivated3":"2326119.2610","SBEP_Metab_Control1":"481045.2352","SBEP_Metab_Control2":"709047.3964","SBEP_Metab_Control3":"789425.1007"},{"Metabolite":"fumaric acid","SBEP_Metab_LPSactivated1":"","SBEP_Metab_LPSactivated2":"","SBEP_Metab_LPSactivated3":"","SBEP_Metab_Control1":"3276814.9275","SBEP_Metab_Control2":"3400546.9545","SBEP_Metab_Control3":"4137408.8530"},{"Metabolite":"glucoheptonic acid","SBEP_Metab_LPSactivated1":"2634651.2925","SBEP_Metab_LPSactivated2":"2829935.9925","SBEP_Metab_LPSactivated3":"2869015.6730","SBEP_Metab_Control1":"1288067.9260","SBEP_Metab_Control2":"1342649.3530","SBEP_Metab_Control3":"1229431.2395"},{"Metabolite":"gluconic acid","SBEP_Metab_LPSactivated1":"494827.0838","SBEP_Metab_LPSactivated2":"699589.9422","SBEP_Metab_LPSactivated3":"617827.3551","SBEP_Metab_Control1":"","SBEP_Metab_Control2":"","SBEP_Metab_Control3":""},{"Metabolite":"glycerol 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