#METABOLOMICS WORKBENCH araskind_20150606_9816311_mwtab.txt DATATRACK_ID:275 STUDY_ID:ST000178 ANALYSIS_ID:AN000274 PROJECT_ID:PR000153 VERSION 1 CREATED_ON 01-15-2019 #PROJECT PR:PROJECT_TITLE Graft-Versus-Host Disease PR:PROJECT_SUMMARY T cell metabolism during graft-versus-host disease PR:INSTITUTE University of Michigan PR:DEPARTMENT Pediatrics PR:LABORATORY Ferrara lab PR:LAST_NAME Byersdorfer PR:FIRST_NAME Craig PR:ADDRESS Ann Arbor, MI PR:EMAIL craigbye@med.umich.edu PR:PHONE 734-000-0000 PR:DOI http://dx.doi.org/10.21228/M8B01C #STUDY ST:STUDY_TITLE T cell metabolism during graft-versus-host disease (CAB 307)-PART I ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) ST:STUDY_SUMMARY T cells were injected into mice to model graft-versus-host disease. On day 7 ST:STUDY_SUMMARY after bone marrow transplantation (BMT), cells were recovered and CD8 T cells ST:STUDY_SUMMARY were purified to > 90% purity over magnetic columns. Naïve T cells were used ST:STUDY_SUMMARY as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with ST:STUDY_SUMMARY anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to ST:STUDY_SUMMARY BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they ST:STUDY_SUMMARY were removed from the plates, counted, and an equal number (2.5x10^6) were ST:STUDY_SUMMARY placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed ST:STUDY_SUMMARY once with ammonium chloride, residual volume was removed by a second brief spin, ST:STUDY_SUMMARY cell pellets were flash frozen in liquid nitrogen and stored at -80oC until ST:STUDY_SUMMARY analysis. Several mice lines were used in this study. 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@umich.edu ST:PHONE - #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:SPECIES_GROUP Mammal #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0004282 S00015097 Treatment:Control SUBJECT_SAMPLE_FACTORS SU0004282 S00015098 Treatment:Control SUBJECT_SAMPLE_FACTORS SU0004282 S00015099 Treatment:Control SUBJECT_SAMPLE_FACTORS SU0004282 S00015100 Treatment:Control SUBJECT_SAMPLE_FACTORS SU0004281 S00015094 Treatment:GVHD SUBJECT_SAMPLE_FACTORS SU0004281 S00015095 Treatment:GVHD SUBJECT_SAMPLE_FACTORS SU0004281 S00015096 Treatment:GVHD #COLLECTION CO:SAMPLE_TYPE Cells CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx SP:SAMPLEPREP_SUMMARY - #CHROMATOGRAPHY CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm.m.zip CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:CHROMATOGRAPHY_TYPE HILIC #ANALYSIS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ANALYSIS_TYPE MS AN:ACQUISITION_PARAMETERS_FILE Column1_solv1_jetstream+_grad9.m.zip AN:PROCESSING_PARAMETERS_FILE EX00317-MassHunterQuant-GlyTCA-DataAnalysis-LCMS-Method.m.zip #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00015097 S00015098 S00015099 S00015100 S00015094 S00015095 S00015096 Factors Treatment:Control Treatment:Control Treatment:Control Treatment:Control Treatment:GVHD Treatment:GVHD Treatment:GVHD 2 or 3-phosphoglycerate_2PG/3PG 1.0582 1.0757 1.0527 0.7890 0.7353 0.6970 0.8304 6-Phosphogluconate Acetyl-CoA ADP 0.1271 0.1945 0.1932 0.1138 0.4625 0.4169 0.3616 AMP 2.5627 4.0507 4.5709 1.4101 8.8678 7.4131 10.9324 ATP 0.1474 0.2738 0.2234 0.1315 0.3448 0.3543 0.3777 Citrate or Isocitrate 1.7984 1.9792 0.9156 0.5452 2.3921 1.9396 2.6428 Erythrose 4-phosphate 1.2877 1.3534 1.4532 0.9039 3.4594 0.6687 0.9078 flavin adenine dinucleotide Fructose 1_6-bisphosphate 0.5827 0.3705 0.2095 0.1099 0.5647 0.6192 0.4534 Glucose 6-phosphate or fructose-6-phosphate 1.1658 0.7431 0.3889 0.2788 1.0281 0.9648 1.0455 Malate 1.3507 1.3001 0.9612 0.4763 3.0497 2.4931 3.5177 Nicotinamide Adenine Dinucleotide oxidized nicotinamide adenine dinucleotide phosphate oxidized nicotinamide adenine dinucleotide phosphate reduced Nicotinamide Adenine Dinucleotide reduced Phosphoenolpyruvate Ribose-5-phosphate or xylulose 5-phosphate 0.4718 0.5340 0.5615 0.3260 3.8181 3.4323 4.7969 sedoheptulose 0.1566 0.1613 0.1174 0.1071 0.1060 0.0393 0.0717 Sedoheptulose 7-phosphate 0.1930 0.1815 0.0810 0.0251 0.4378 0.4773 0.2842 Sucrose 0.2185 0.3110 0.2436 0.1519 0.2951 0.2647 0.3271 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name pubchem_id inchi_key kegg_id other_id other_id_type ri ri_type moverz_quant 2 or 3-phosphoglycerate_2PG/3PG 724 C00597 2PG/3PG UM_Target_ID 6-Phosphogluconate 91493 C00345 6PG UM_Target_ID Acetyl-CoA 444493 C00024 aCoA UM_Target_ID ADP 6022 C00008 ADP UM_Target_ID AMP 6083 C00020 AMP UM_Target_ID ATP 5957 C00002 ATP UM_Target_ID Citrate or Isocitrate 311 C00158 CIT/ICIT UM_Target_ID Erythrose 4-phosphate 122357 C00279 E4P UM_Target_ID flavin adenine dinucleotide 643975 C00016 FAD UM_Target_ID Fructose 1,6-bisphosphate 172313 C00354 FBP UM_Target_ID Glucose 6-phosphate or fructose-6-phosphate 5958 C00092 G6P/F6P UM_Target_ID Malate 222656 C00149 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 10897651 C00003 NAD UM_Target_ID nicotinamide adenine dinucleotide phosphate oxidized 5886 C00006 NADP UM_Target_ID nicotinamide adenine dinucleotide phosphate reduced 5886 C00006 NADPH UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 C00004 NADH UM_Target_ID Phosphoenolpyruvate 1005 C00074 PEP UM_Target_ID Ribose-5-phosphate or xylulose 5-phosphate 77982 C00117 R5P/X5P UM_Target_ID sedoheptulose 102926 SED UM_Target_ID Sedoheptulose 7-phosphate 165007 C05382 S7P UM_Target_ID Sucrose 5988 C00089 SUC UM_Target_ID METABOLITES_END #END