#METABOLOMICS WORKBENCH araskind_20150607_9529581_mwtab.txt DATATRACK_ID:282 STUDY_ID:ST000278 ANALYSIS_ID:AN000444 PROJECT_ID:PR000222 VERSION 1 CREATED_ON 01-15-2019 #PROJECT PR:PROJECT_TITLE Viral Effect on Metabolism PR:PROJECT_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) PR:PROJECT_SUMMARY Global Metabolic profiling of infection by respiratory virus PR:INSTITUTE University of Texas Medical Branch PR:DEPARTMENT Department of Pediatrics PR:LABORATORY Casola Lab PR:LAST_NAME Casola PR:FIRST_NAME Antonella PR:ADDRESS Galveston, TX PR:EMAIL yazhao1@utmb.edu PR:PHONE 409-772-2798 PR:DOI http://dx.doi.org/10.21228/M8TP4R #STUDY ST:STUDY_TITLE Viral Effect on Metabolism (part I) ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) ST:STUDY_SUMMARY Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown ST:STUDY_SUMMARY according to the manufacturer's instructions in growth medium (SAGM) containing ST:STUDY_SUMMARY 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml ST:STUDY_SUMMARY hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml ST:STUDY_SUMMARY retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml ST:STUDY_SUMMARY Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When ST:STUDY_SUMMARY SAE grew to around 80 to 90% confluence, the cells were put into basal medium ST:STUDY_SUMMARY not supplemented with growth factors 3hours. Then the cell monolayers were ST:STUDY_SUMMARY infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain ST:STUDY_SUMMARY time. The supernatant was saved and cells were harvested and stored exactly ST:STUDY_SUMMARY according to the protocol provided by University of Michigan Metabolomics Core ST:STUDY_SUMMARY Facility for metabolomics analysis. 50mM ammonium acetate in water was used for ST:STUDY_SUMMARY rinse buffer. ST:INSTITUTE University of Michigan ST:DEPARTMENT Department of Pediatrics ST:LABORATORY Casola Lab (University of Texas Medical Branch) ST:LAST_NAME Zhao ST:FIRST_NAME Yanhua ST:ADDRESS Galveston, TX ST:EMAIL yazhao1@utmb.edu ST:PHONE 409-443-1461 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:SPECIES_GROUP Human #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - S00016664 INFECTION TIME (0-24 Hrs):0 SUBJECT_SAMPLE_FACTORS - S00016665 INFECTION TIME (0-24 Hrs):0 SUBJECT_SAMPLE_FACTORS - S00016666 INFECTION TIME (0-24 Hrs):0 SUBJECT_SAMPLE_FACTORS - S00016670 INFECTION TIME (0-24 Hrs):15 SUBJECT_SAMPLE_FACTORS - S00016671 INFECTION TIME (0-24 Hrs):15 SUBJECT_SAMPLE_FACTORS - S00016672 INFECTION TIME (0-24 Hrs):15 SUBJECT_SAMPLE_FACTORS - S00016673 INFECTION TIME (0-24 Hrs):24 SUBJECT_SAMPLE_FACTORS - S00016674 INFECTION TIME (0-24 Hrs):24 SUBJECT_SAMPLE_FACTORS - S00016675 INFECTION TIME (0-24 Hrs):24 SUBJECT_SAMPLE_FACTORS - S00016667 INFECTION TIME (0-24 Hrs):6 SUBJECT_SAMPLE_FACTORS - S00016668 INFECTION TIME (0-24 Hrs):6 SUBJECT_SAMPLE_FACTORS - S00016669 INFECTION TIME (0-24 Hrs):6 #COLLECTION CO:SAMPLE_TYPE Cell Line 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 AQM011 CH:METHODS_FILENAME ALPHA_KETO_ACIDS-FULL.M.zip CH:INSTRUMENT_NAME Agilent 7890A CH:COLUMN_NAME Agilent DB5-MS (30m × 0.25mm, 0.25um) CH:CHROMATOGRAPHY_TYPE GC #ANALYSIS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ANALYSIS_TYPE MS AN:ACQUISITION_PARAMETERS_FILE ALPHA_KETO_ACIDS-FULL.M AN:PROCESSING_PARAMETERS_FILE EX00368-MassHunterQuant-GlyTCA-GC-DataAnalysis-Method.m #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 5975C MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE EI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00016664 S00016665 S00016666 S00016670 S00016671 S00016672 S00016673 S00016674 S00016675 S00016667 S00016668 S00016669 Factors INFECTION TIME (0-24 Hrs):0 INFECTION TIME (0-24 Hrs):0 INFECTION TIME (0-24 Hrs):0 INFECTION TIME (0-24 Hrs):15 INFECTION TIME (0-24 Hrs):15 INFECTION TIME (0-24 Hrs):15 INFECTION TIME (0-24 Hrs):24 INFECTION TIME (0-24 Hrs):24 INFECTION TIME (0-24 Hrs):24 INFECTION TIME (0-24 Hrs):6 INFECTION TIME (0-24 Hrs):6 INFECTION TIME (0-24 Hrs):6 2 or 3-phosphoglycerate_2PG/3PG 7.2109 9.7729 7.7790 5.2016 5.5646 1.3556 3.3472 3.4783 1.8669 9.6603 7.5538 2.8449 6-Phosphogluconate 12.9604 6.7689 6.2816 4.3382 3.8711 6.3997 3.0625 2.4734 7.4679 6.2478 6.4986 10.5775 Acetyl-CoA 1.7585 0.8326 1.5402 3.1571 2.3604 1.9365 2.5062 1.8294 2.0880 1.5909 1.3377 1.7598 ADP 245.6842 69.7823 43.5638 91.0441 48.2167 117.7878 73.9733 54.6068 122.2846 68.6124 86.7148 124.3525 AMP 598.8894 63.5573 51.2755 72.7866 44.5056 547.0729 81.7956 51.3098 595.5468 56.3010 104.7472 630.6231 ATP 1080.4268 1065.0704 1046.1997 1249.5687 858.1284 387.3420 764.9316 674.6677 438.3552 1153.6452 1043.5216 503.2715 Citrate or Isocitrate 62.5318 41.2233 46.9292 85.2503 73.2136 57.9834 69.0360 63.8405 63.8592 87.4194 94.3143 82.4112 Erythrose 4-phosphate 47.7812 11.9974 13.9048 26.1320 22.2451 28.3171 28.2715 19.4888 32.1705 12.9763 21.8987 28.2255 flavin adenine dinucleotide 1.3376 0.9147 0.9510 1.3242 0.9666 0.7568 0.9203 0.9364 0.9441 1.2015 1.3112 0.8748 Fructose 1_6-bisphosphate 108.1136 111.4112 118.5792 78.2383 54.1404 18.0183 61.4530 44.5080 31.6988 121.2532 130.3715 42.5975 Glucose 6-phosphate or fructose-6-phosphate 60.8559 24.1002 23.4547 36.3224 25.6044 47.0266 29.4174 23.3227 48.7322 26.3124 31.5395 46.0598 Malate 130.8806 87.9238 93.5793 66.7578 55.5441 41.9971 61.5242 54.5337 55.8292 90.7693 104.7536 79.8110 Nicotinamide Adenine Dinucleotide oxidized 53.0273 38.0305 41.3879 48.6584 41.4074 31.5627 40.0170 36.0201 35.2974 51.8479 57.7828 41.5902 nicotinamide adenine dinucleotide phosphate oxidized 6.5771 4.0963 2.0516 4.2182 2.5302 1.1994 2.9342 2.7724 1.8145 4.4684 4.7466 2.5694 nicotinamide adenine dinucleotide phosphate reduced 10.0757 14.1021 23.2088 3.3065 4.4625 5.6311 1.5999 2.6634 4.5383 15.3767 11.0840 8.0404 Nicotinamide Adenine Dinucleotide reduced 2.2301 1.9131 2.0502 1.9884 2.4391 0.8479 2.1915 1.7679 1.1794 2.5533 2.3334 1.6383 Phosphoenolpyruvate 5.9215 5.4430 2.9224 1.8618 6.5652 3.2979 1.9664 Ribose-5-phosphate or xylulose 5-phosphate 19.9947 8.3260 9.9041 4.5804 4.1234 5.7074 3.9264 3.4377 8.0134 6.3096 6.7745 10.8920 Sedoheptulose 7-phosphate 17.2203 9.8083 10.2597 8.5466 6.8516 5.9966 5.6136 5.9673 7.9714 8.9946 9.9055 9.7725 Sucrose 11.2973 4.6264 5.2165 8.3815 7.3135 10.5954 7.7392 6.0837 11.8511 7.9132 6.9373 13.7809 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 7-phosphate 165007 C05382 S7P UM_Target_ID Sucrose 5988 C00089 SUC UM_Target_ID METABOLITES_END #END