#METABOLOMICS WORKBENCH araskind_20170802_184250 DATATRACK_ID:1186 STUDY_ID:ST000835 ANALYSIS_ID:AN001337 PROJECT_ID:PR000595 VERSION 1 CREATED_ON August 9, 2017, 9:44 am #PROJECT PR:PROJECT_TITLE Influence of murine norovirus on cell metabolism PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY C6_effects_in_RAW PR:INSTITUTE University of Michigan PR:DEPARTMENT Microbiology & Immunology PR:LABORATORY Passalacqua Lab PR:LAST_NAME Passalacqua PR:FIRST_NAME Karla PR:ADDRESS Ann Arbor, MI PR:EMAIL kpassal@umich.edu PR:PHONE 734-763-5639 #STUDY ST:STUDY_TITLE Deubiquitinase inhibitor compound C6 effect on cellular metabolism ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY 6.0 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to ST:STUDY_SUMMARY recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, ST:STUDY_SUMMARY and 12 mL of fresh medium with either 2.5 micromolar Compound C6 or a v/v match ST:STUDY_SUMMARY of DMSO (vehicle control) was added to the cells. Cells were incubated at 37 ST:STUDY_SUMMARY degrees in 5% CO2 for 30 minutes. Cells were washed 3X with cold DPBS++ and 10 ST:STUDY_SUMMARY mL of medium was added to the cells with either 1.0 micromolar Compound C6 or ST:STUDY_SUMMARY v/v match of DMSO. Cells were incubated at 37 degrees and 5% CO2 for 7.0 hours. ST:STUDY_SUMMARY Cells were washed with 10 mL of 150 mM Ammonium Acetate, swirled, washed again ST:STUDY_SUMMARY with 5 mL, and immediately quenched with liquid nitrogen. Cells were then frozen ST:STUDY_SUMMARY at -80 degrees. ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@med.umich.edu ST:PHONE (734) 232-8175 ST:NUM_GROUPS 7 ST:TOTAL_SUBJECTS 1 ST:STUDY_COMMENTS I request that the metabolites of the TCA+ assay that are to be assessed ST:STUDY_COMMENTS quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, ST:STUDY_COMMENTS E4P, S7P, 6PG, G3P, H6P, and Lactate in particular. Also, I would request that ST:STUDY_COMMENTS both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be ST:STUDY_COMMENTS included in the non-quantitative data. #SUBJECT SU:SUBJECT_TYPE MOUSE SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0016447 S00026310 Sample type:Cell Line | Treatment:Vehicle | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026311 Sample type:Cell Line | Treatment:Vehicle | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026312 Sample type:Cell Line | Treatment:Vehicle | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026313 Sample type:Cell Line | Treatment:Vehicle | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026314 Sample type:Cell Line | Treatment:Vehicle | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026315 Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026316 Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026317 Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026318 Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026319 Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW SUBJECT_SAMPLE_FACTORS SU0016447 S00026320 Sample type:Macrophages | Treatment:Control-Other_Cells | Type:Primary BL6 BMM SUBJECT_SAMPLE_FACTORS SU0016447 S00026321 Sample type:Macrophages | Treatment:Control-Other_Cells | Type:Primary BL6 BMM #COLLECTION CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME A043-TCA-Plus-20170713.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A043-TCA-Plus-20170713.pdf #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6520B QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/ug protein MS_METABOLITE_DATA_START Samples S00026310 S00026311 S00026312 S00026313 S00026314 S00026315 S00026316 S00026317 S00026318 S00026319 S00026320 S00026321 Factors Sample type:Cell Line | Treatment:Vehicle | Type:RAW Sample type:Cell Line | Treatment:Vehicle | Type:RAW Sample type:Cell Line | Treatment:Vehicle | Type:RAW Sample type:Cell Line | Treatment:Vehicle | Type:RAW Sample type:Cell Line | Treatment:Vehicle | Type:RAW Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW Sample type:Cell Line | Treatment:DUB inhibitor | Type:RAW Sample type:Macrophages | Treatment:Control-Other_Cells | Type:Primary BL6 BMM Sample type:Macrophages | Treatment:Control-Other_Cells | Type:Primary BL6 BMM D-ERYTHROSE 4-PHOSPHATE 65.77136345 72.69431591 70.07112106 89.5901296 103.9879774 52.15642498 56.73698563 30.9851976 55.0910399 46.43563075 8.178732848 6.608272271 BETA-NAD+ 1.356641362 22.91536151 19.85965431 25.5208771 26.30553486 12.75756093 15.87727484 12.6108478 21.67774206 20.61688626 COENZYME II 10.78670728 11.07632086 9.166335501 13.0659772 13.29684073 6.680043548 7.550718826 6.159200917 9.122171286 8.911876332 .311106127 .193843661 SEDOHEPTULOSE 7-PHOSPHATE 4.591960664 8.552768894 5.639966154 6.563507353 7.836592468 4.084002949 3.42722215 1.995207731 2.620634725 2.579196416 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) 72.87404629 54.44270741 64.53492682 102.8837235 108.460238 36.93846124 58.78375005 47.79778851 73.17184955 72.82126132 71.8880279 53.64516349 NADP-REDUCED 2.234612151 .712546854 6.533823982 5.895334876 3.821929955 1.868191367 4.560717405 .655653159 CITRIC ACID 165.2134181 164.0222421 147.2515328 193.9864067 206.8948533 111.5943225 134.2895385 100.7484648 160.514514 139.6852278 79.05084073 66.19387626 NADH 1.223411225 .440471234 .785423721 1.014554841 .90983301 .888449468 2.202173641 .683298071 1.454594791 1.417533364 FAD 1.437238823 2.237986654 1.716376708 2.178365312 2.672149923 1.198824771 1.716458314 1.475086202 1.920766018 2.186202861 .739782721 .581640321 MALIC ACID 138.5110725 184.6284558 167.8444542 173.0992077 169.4483032 77.94214803 97.12196478 84.38557315 122.7309369 101.2412045 24.97101452 19.10548833 ADENOSINE TRIPHOSPHATE 1239.651807 1329.044892 1065.035636 1784.616466 1794.403556 851.7267116 1079.55322 766.1723153 1145.779994 1036.211262 108.2144886 52.87510131 ROBISON ESTER 85.63828814 114.3333961 97.2512773 115.6366819 124.4895896 62.01365427 76.17659632 77.71051876 75.61192514 75.4169011 37.06496998 35.95107359 SUCROSE 100.4114044 143.2393674 63.17648665 140.653108 150.3616616 56.79888988 62.50403065 37.24275387 64.70781119 67.68691234 ADENOSINE 5'-DIPHOSPHATE 181.5707243 219.8191795 186.6283137 194.5044221 184.191426 91.8924289 121.0621435 107.5505923 132.922589 122.583518 20.94736605 15.16934311 ADENOSINE 5'-MONOPHOSPHATE 24.24367595 39.99843917 31.84620665 38.57590392 32.49502447 20.45299571 25.0656325 30.48013025 28.20792907 29.64824095 84.12109774 64.23700623 GLYCERATE 3-PHOSPHATE 74.0289812 49.04141452 34.26735862 139.3849976 14.40305969 15.81468184 32.52951627 52.81925934 65.14285554 25.93475004 RIBOSE PHOSPHATE 10.69013611 17.2605565 11.12482961 14.79394662 14.56946251 9.614025205 8.356729698 8.451977136 10.279775 9.403634038 6-PHOSPHOGLUCONIC ACID 25.24889965 38.2639946 29.16242414 36.46139811 37.12528303 28.33180845 26.16496561 24.86636804 22.5195166 20.68470197 1.598239805 .577927735 ACETOACETYL-COA .36839638 .309914197 .235305205 .347413594 .409800166 .074058678 .162924758 .020982436 .215905669 .257728523 .167231242 .339919738 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type D-ERYTHROSE 4-PHOSPHATE 122357 BETA-NAD+ 15938971 COENZYME II 15938972 SEDOHEPTULOSE 7-PHOSPHATE 165007 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) 21125049 NADP-REDUCED 22833512 CITRIC ACID 311 NADH 439153 FAD 46906035 MALIC ACID 525 ADENOSINE TRIPHOSPHATE 5957 ROBISON ESTER 5958 SUCROSE 5988 ADENOSINE 5'-DIPHOSPHATE 6022 ADENOSINE 5'-MONOPHOSPHATE 6083 GLYCERATE 3-PHOSPHATE 724 RIBOSE PHOSPHATE 77982 6-PHOSPHOGLUCONIC ACID 91493 ACETOACETYL-COA 92153 METABOLITES_END #END