#METABOLOMICS WORKBENCH araskind_20150607_9556221_mwtab.txt DATATRACK_ID:280 STUDY_ID:ST000183 ANALYSIS_ID:AN000281 PROJECT_ID:PR000219 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE Metabolic regulation by PARP-1 in myofibroblast differentiation and fibrosis PR:PROJECT_SUMMARY Analysis of wild type lung tissue after saline or bleomycin treatment PR:INSTITUTE University of Michigan PR:DEPARTMENT Deaprtment of Pathology PR:LABORATORY Sem H. Phan PR:LAST_NAME Hu PR:FIRST_NAME Biao PR:ADDRESS Ann Arbor, MI PR:EMAIL biaohu@med.umich.edu PR:PHONE 734-7635731 #STUDY ST:STUDY_TITLE Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human ST:STUDY_TITLE & Normal Lung Fiboblasts 3 ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis (especially interested in ST:STUDY_TYPE and NAD+ and related metabolite analysis for all samples ST:STUDY_SUMMARY Glycolysis/TCA/Nucleotide analysis (especially interested in ST:STUDY_SUMMARY and NAD+ and related metabolite analysis for all samples 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 - ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 16 #SUBJECT SU:SUBJECT_TYPE - 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 SU0004503 S00015480 wt B6:N | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004504 S00015481 wt B6:N | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004505 S00015482 wt B6:N | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004506 S00015483 wt B6:N | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004507 S00015484 wt B6:N | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004498 S00015475 wt B6:N | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004499 S00015476 wt B6:N | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004500 S00015477 wt B6:N | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004501 S00015478 wt B6:N | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004502 S00015479 wt B6:N | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004494 S00015471 wt B6:Y | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004495 S00015472 wt B6:Y | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004496 S00015473 wt B6:Y | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004497 S00015474 wt B6:Y | saline/HLF:N | bleomycin/IPF:Y SUBJECT_SAMPLE_FACTORS SU0004492 S00015469 wt B6:Y | saline/HLF:Y | bleomycin/IPF:N SUBJECT_SAMPLE_FACTORS SU0004493 S00015470 wt B6:Y | saline/HLF:Y | bleomycin/IPF:N #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Cells #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm.m.zip #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ACQUISITION_PARAMETERS_FILE QTOF-002-HILIC-35min-1mm.m.zip AN:PROCESSING_PARAMETERS_FILE EX00331-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 µM MS_METABOLITE_DATA_START Samples S00015480 S00015481 S00015482 S00015483 S00015484 S00015475 S00015476 S00015477 S00015478 S00015479 S00015471 S00015472 S00015473 S00015474 S00015469 S00015470 Factors wt B6:N | saline/HLF:N | bleomycin/IPF:Y wt B6:N | saline/HLF:N | bleomycin/IPF:Y wt B6:N | saline/HLF:N | bleomycin/IPF:Y wt B6:N | saline/HLF:N | bleomycin/IPF:Y wt B6:N | saline/HLF:N | bleomycin/IPF:Y wt B6:N | saline/HLF:Y | bleomycin/IPF:N wt B6:N | saline/HLF:Y | bleomycin/IPF:N wt B6:N | saline/HLF:Y | bleomycin/IPF:N wt B6:N | saline/HLF:Y | bleomycin/IPF:N wt B6:N | saline/HLF:Y | bleomycin/IPF:N wt B6:Y | saline/HLF:N | bleomycin/IPF:Y wt B6:Y | saline/HLF:N | bleomycin/IPF:Y wt B6:Y | saline/HLF:N | bleomycin/IPF:Y wt B6:Y | saline/HLF:N | bleomycin/IPF:Y wt B6:Y | saline/HLF:Y | bleomycin/IPF:N wt B6:Y | saline/HLF:Y | bleomycin/IPF:N 2 or 3-phosphoglycerate_2PG/3PG 1.0550 1.1364 1.6313 1.3068 1.2689 1.1185 1.3370 1.5969 1.4706 1.0635 0.8683 1.1283 1.1247 0.8061 0.6900 0.6753 Acetyl-CoA 0.0258 0.0128 0.0107 0.0166 0.0128 0.0326 0.0110 0.0198 0.0313 0.0276 0.1256 0.0944 0.1456 0.1520 0.1490 0.1693 ADP 5.6182 5.8950 5.8488 5.8451 6.2207 4.6881 4.5223 3.6985 4.1268 3.8256 7.2680 6.4957 7.0486 5.4952 5.4227 4.6861 Alanine 2.0681 1.3206 1.1158 4.0713 0.5943 1.0898 1.3225 1.1751 1.6512 4.2169 7.7223 4.4421 7.3235 2.1492 2.4597 alpha-Ketoglutarate 0.2646 0.2454 0.2403 0.2663 0.2405 0.2505 0.2586 0.2526 0.2508 0.2288 0.2309 0.2360 0.2381 0.2251 0.2280 AMP 79.3701 92.8967 80.2425 117.2987 110.3205 28.2703 24.1586 22.7265 24.9199 24.3240 139.1803 84.5408 217.2952 203.8000 407.2229 326.8086 Aspartate 6.3080 4.6913 3.7597 10.8571 4.8688 8.2219 8.0346 8.0066 12.4270 108.3570 208.5936 125.9085 193.9844 82.2288 83.1218 ATP 11.1993 12.6165 11.1297 9.3763 11.2626 24.2645 22.0586 19.2175 20.1239 21.5044 1.4067 1.8129 1.3926 1.0409 1.1036 0.5494 Citrate or Isocitrate 4.2950 4.5753 3.8840 3.3337 3.8567 5.8992 5.7513 5.9813 5.7827 5.7547 23.9833 30.5927 21.2212 18.1183 15.5953 16.8493 Erythrose 4-phosphate 4.9664 6.1585 8.5747 5.0410 5.2846 7.1859 7.6633 7.3595 7.6626 5.3615 24.8971 41.3395 26.9067 18.9360 20.0382 18.4632 flavin adenine dinucleotide 0.1980 0.1795 0.2031 0.1895 0.1953 0.0959 0.1210 0.1206 0.1089 0.1081 0.5867 0.6589 0.5708 0.4885 0.5638 0.5387 Fructose 1_6-bisphosphate 11.7212 12.3808 10.1832 9.9282 10.8642 11.3643 10.7416 11.1568 10.3132 11.2266 9.3443 15.5613 10.9592 7.0867 6.3724 5.4398 fumarate 2.8390 2.8076 2.7885 3.1032 2.8785 2.7818 2.7896 2.7916 2.8256 4.8130 5.2063 4.7342 7.0043 3.8292 3.9963 Glucose 6-phosphate or fructose-6-phosphate 5.2816 5.8430 7.5404 3.8792 4.7754 5.6628 3.1875 3.2626 2.8043 2.9538 36.9744 60.6100 41.2033 26.9268 32.1022 29.3824 Glutamate 3.9098 2.9760 2.4429 6.6109 2.8702 4.8957 4.7753 4.8792 6.8351 8.6937 14.2910 8.9094 14.3780 6.3029 6.1040 glutamine 14.9009 10.1473 8.7444 22.6340 11.6923 20.7194 21.1580 22.8250 29.6827 19.4185 31.9335 13.3502 19.5133 6.8331 6.4461 Lactate 1.5286 0.3026 0.1892 4.6088 0.0000 0.3732 1.0560 1.1605 0.9432 1.9041 3.0102 2.9743 6.3374 0.0000 0.0000 Malate 5.9355 7.1126 8.3023 6.9308 7.2478 5.8924 4.9491 5.7229 5.8796 6.0309 107.9042 158.9935 112.0565 77.0801 58.5476 61.3382 Nicotinamide Adenine Dinucleotide oxidized 1.3798 1.4030 1.1507 1.3779 1.5334 2.0002 1.8844 1.7881 1.4416 1.9292 0.0553 0.0123 0.0523 0.0430 0.0214 nicotinamide adenine dinucleotide phosphate oxidized 0.2324 0.2723 0.2254 0.3246 0.2858 0.1601 0.1518 0.1489 0.1576 0.1452 0.4093 0.2941 0.2866 0.3482 0.3066 0.3737 Nicotinamide Adenine Dinucleotide reduced 0.3096 0.3762 0.5646 0.4539 0.3930 0.7821 1.5549 1.6839 1.6166 0.8677 0.1871 0.2157 0.1964 0.1748 0.1593 0.1161 Oxaloacetate 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 0.1944 Phosphoenolpyruvate 0.1120 0.0971 0.2333 0.1411 0.1397 0.0958 0.1273 0.2626 0.1785 0.0632 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 pyruvate 1.2304 1.2203 1.2240 1.2459 1.2510 1.2535 1.2427 1.2166 1.2241 1.2344 1.2365 1.2121 1.2123 Ribose-5-phosphate or xylulose 5-phosphate 6.6111 8.8571 11.8220 7.2820 9.6030 6.3307 6.2182 9.6120 6.5956 7.3135 22.1143 40.0006 27.7093 15.8785 13.0958 13.1631 Sedoheptulose 7-phosphate 1.1543 1.2961 1.5113 1.5292 1.4074 0.8841 0.7140 0.8641 0.7320 0.7307 9.4201 13.6888 9.2062 6.6866 5.9628 6.2186 Sucrose 0.8441 0.9521 1.4247 0.9968 0.9296 1.4054 1.3932 1.5294 1.4947 1.2300 0.9310 1.2047 1.4065 0.8448 0.9888 0.9008 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 2 or 3-phosphoglycerate_2PG/3PG 724 2PG/3PG UM_Target_ID Acetyl-CoA 444493 aCoA UM_Target_ID ADP 6022 ADP UM_Target_ID Alanine 5950 ALA UM_Target_ID alpha-Ketoglutarate 51 AKG UM_Target_ID AMP 6083 AMP UM_Target_ID Aspartate 424 ASP UM_Target_ID ATP 5957 ATP UM_Target_ID Citrate or Isocitrate 311 CIT/ICIT UM_Target_ID Erythrose 4-phosphate 122357 E4P UM_Target_ID flavin adenine dinucleotide 46906035 FAD UM_Target_ID Fructose 1,6-bisphosphate 21125049 FBP UM_Target_ID fumarate 444972 FUM UM_Target_ID Glucose 6-phosphate or fructose-6-phosphate 5958 G6P/F6P UM_Target_ID Glutamate 611 GLU UM_Target_ID glutamine 5961 GLN UM_Target_ID Lactate 612 LAC UM_Target_ID Malate 525 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 15938971 NAD UM_Target_ID nicotinamide adenine dinucleotide phosphate oxidized 15938972 NADP UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 NADH UM_Target_ID Oxaloacetate 970 OAA UM_Target_ID Phosphoenolpyruvate 1005 PEP UM_Target_ID pyruvate 1060 PYR UM_Target_ID Ribose-5-phosphate or xylulose 5-phosphate 77982 R5P/X5P UM_Target_ID Sedoheptulose 7-phosphate 165007 S7P UM_Target_ID Sucrose 5988 SUC UM_Target_ID METABOLITES_END #END