#METABOLOMICS WORKBENCH araskind_20170619_105956 DATATRACK_ID:985 STUDY_ID:ST000690 ANALYSIS_ID:AN001065 PROJECT_ID:PR000489 VERSION 1 CREATED_ON June 30, 2017, 3:11 pm #PROJECT PR:PROJECT_TITLE Human oral keratinocytes growth and proliferation based on culture medium volume PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY Using different culture medium volume to affect cultured human oral PR:PROJECT_SUMMARY keratinocytes growth and proliferation rates PR:INSTITUTE University of Michigan PR:DEPARTMENT Oral & Maxillofacial Surgery PR:LABORATORY Feinberg Lab PR:LAST_NAME Feinberg PR:FIRST_NAME Stephen PR:ADDRESS Ann Arbor, MI PR:EMAIL sefein@umich.edu PR:PHONE 734-763-5963 #STUDY ST:STUDY_TITLE Human oral keratinocytes growth and proliferation based on culture medium volume ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY We seeded cells at density of 500k/T75 and cultured them at two different medium ST:STUDY_SUMMARY volume, one at 30ml, the other at 15ml. Culture medium is composed of 1x EDGS ST:STUDY_SUMMARY and 0.06mM calcium. We changed medium every day for 30ml culture, and every two ST:STUDY_SUMMARY days for 15ml culture. We collected spent medium when we changed medium. The ST:STUDY_SUMMARY collected spent medium was filtered through low protein binding 0.22um pore size ST:STUDY_SUMMARY filter and then stored at -80 degree C. For OA and SMT, spent medium was ST:STUDY_SUMMARY collected on the same day of D5 and D9 after cell seeding as marked on the ST:STUDY_SUMMARY tubes. For GK samples, 15ml and 30ml cultures were collected when cells reached ST:STUDY_SUMMARY at around 90% confluence, that is D5 for 15ml and D6 for 30 ml culture. The ST:STUDY_SUMMARY numbers 151, 152 were duplicated cell cultures in two T75s, same for 301 and ST:STUDY_SUMMARY 302. One major differences among GK, OA, and SMT is GK was from frozen cells; OA ST:STUDY_SUMMARY and SMT were fresh cells that were never frozen. Blank15 and Blank30 were ST:STUDY_SUMMARY complete medium without cells incubating in incubator for two days for Blank15 ST:STUDY_SUMMARY and one day for Blank30. Medium was collected in the same manner as others. 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 10 ST:TOTAL_SUBJECTS 5 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0003722 S00014307 Day:5 days | Line:GK | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014308 Day:5 days | Line:GK | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014309 Day:6 days | Line:GK | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014310 Day:6 days | Line:GK | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014311 Day:5 days | Line:OA | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014312 Day:9 days | Line:OA | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014313 Day:5 days | Line:OA | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014314 Day:9 days | Line:OA | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014315 Day:5 days | Line:SMT | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014316 Day:9 days | Line:SMT | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014317 Day:5 days | Line:SMT | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014318 Day:9 days | Line:SMT | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003725 S00014319 Day:2 days | Line:Blank | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003725 S00014320 Day:2 days | Line:Blank | Volume:30ml SUBJECT_SAMPLE_FACTORS SU9999996 S00020128 Day:- | Line:- | Volume:- #COLLECTION CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME A003 - Untargeted Metabolomics.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Waters Acquity HSS T3 (50 x 2.1mm, 1.8um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A003 - Untargeted Metabolomics.pdf #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 peak area MS_METABOLITE_DATA_START Samples S00014307 S00014308 S00014309 S00014310 S00014311 S00014312 S00014313 S00014314 S00014315 S00014316 S00014317 S00014318 S00014319 S00014320 Factors Day:5 days | Line:GK | Volume:15ml Day:5 days | Line:GK | Volume:15ml Day:6 days | Line:GK | Volume:30ml Day:6 days | Line:GK | Volume:30ml Day:5 days | Line:OA | Volume:15ml Day:9 days | Line:OA | Volume:15ml Day:5 days | Line:OA | Volume:30ml Day:9 days | Line:OA | Volume:30ml Day:5 days | Line:SMT | Volume:15ml Day:9 days | Line:SMT | Volume:15ml Day:5 days | Line:SMT | Volume:30ml Day:9 days | Line:SMT | Volume:30ml Day:2 days | Line:Blank | Volume:15ml Day:2 days | Line:Blank | Volume:30ml 3-HYDROXY-3-METHYL-GLUTARIC ACID 96569 94464 1007 109982 1684 87248 1 3-INDOLEACETIC ACID 37965 36775 45382 41381 26230 13864 22645 20284 35163 17119 33653 25737 4811 4-METHYL-2-OXOPENTANOATE 1102856 938236 1252565 1098589 893444 1164019 560450 1265825 1419147 780241 729913 1190012 1 5-OXOPROLINE 34000000 33400000 35000000 33800000 35200000 29400000 33700000 35400000 35600000 30000000 33100000 29200000 30000000 22800000 5?-DEOXY-5?-(METHYLTHIO)ADENOSINE 300116 349114 242770 223487 275933 187735 145717 384808 241378 194394 132044 246277 1 ADENINE 4432338 4271630 5341802 5191583 4797486 3603654 4858353 5136602 4912430 3841044 4849092 4388055 4590274 3726021 CITRAMALIC ACID 140058 123573 149154 132462 83953 67372 81527 110031 100630 72229 91330 64107 65414 18907 CITRIC ACID 915967 1035145 382886 301915 179465 2072210 22372 745169 357931 1332302 107343 427336 5621 23928 FOLIC ACID 37285 34939 36878 35339 33087 29945 30265 44473 36113 32405 33154 31450 25150 16777 FRUCTOSE (M-H) 502850 379687 1992626 2105967 2081242 151444 2713072 926251 1588196 135519 2644573 1481969 3240435 3247787 GLYCERIC ACID 1 1 4757 1699 1 5339 2900 5461 HYPOXANTHINE 180809 211365 104537 66592 14791 215592 20092 75393 76226 162457 84546 1 ISOLEUCINE 95846 85802 130752 133998 124982 29976 138415 129641 113894 74458 140357 89255 139261 83579 L-NORLEUCINE 50051 45721 90333 133998 78881 29981 89678 129641 71009 35389 94890 55927 101145 62633 N-ACETYL-DL-GLUTAMIC ACID 477873 472933 185159 182027 358827 527373 193577 447567 414822 320222 179714 191505 15077 13089 N-ACETYL-L-ALANINE 1 56170 1 72768 1 N-ACETYLGALACTOSAMINE (M-H) 1 71929 14994 27336 10595 35859 29110 41361 9342 1 N-ACETYLGLYCINE 4638 2850 2867 3403 1 2199 2465 2924 2822 1891 N-METHYL-D-ASPARTIC ACID 1 1 39783 29783 1059 53074 51806 71081 33663 8273 7920 PANTOTHENIC ACID 90306 82982 95166 89088 82948 74071 77074 115402 90511 76735 80479 74918 62371 41268 PYRUVIC ACID 276317 258546 208369 195039 179629 314628 155233 221375 235519 267810 167888 212146 34615 58787 SUCCINATE 53385 55221 23785 19813 14965 81663 13368 36714 26536 60558 14275 24422 5976 5024 THYMIDINE 1 3350 10135 61732 157851 3591 9638 115961 195365 137341 URIC ACID 1 1 1 496979 1 URIDINE (M-H) 139185 137681 184215 173538 120159 169142 119786 175857 122215 138661 142388 128960 19748 18659 XANTHINE 420005 447912 232063 178327 49575 627774 18102 347103 186903 549225 95429 294395 1280 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 3-HYDROXY-3-METHYL-GLUTARIC ACID 162.0522 1.574 1662 3-INDOLEACETIC ACID 175.0628 6.841 802 4-METHYL-2-OXOPENTANOATE 130.0631 4.845 70 5-OXOPROLINE 129.0427 1.171 7405 5?-DEOXY-5?-(METHYLTHIO)ADENOSINE 297.089 4.477 439176 ADENINE 135.0545 0.869 190 CITRAMALIC ACID 148.0368 1.396 441696 CITRIC ACID 192.0271 1.003 311 FOLIC ACID 441.1394 5.825 6037 FRUCTOSE (M-H) 180.0635 0.66 5984 GLYCERIC ACID 106.0269 0.806 439194 HYPOXANTHINE 136.0378 1.104 790 ISOLEUCINE 131.0941 1.493 6306 L-NORLEUCINE 131.0944 1.579 21236 N-ACETYL-DL-GLUTAMIC ACID 189.0635 1.286 185 N-ACETYL-L-ALANINE 131.0574 1.49 88064 N-ACETYLGALACTOSAMINE (M-H) 221.0895 0.695 35717 N-ACETYLGLYCINE 117.0419 1.142 1097 N-METHYL-D-ASPARTIC ACID 147.0529 0.792 4376 PANTOTHENIC ACID 219.1105 3.286 6613 PYRUVIC ACID 88.0166 0.972 1060 SUCCINATE 118.0267 1.301 1110 THYMIDINE 242.0903 2.738 5789 URIC ACID 168.0276 0.994 1175 URIDINE (M-H) 244.0696 1.324 6029 XANTHINE 152.0334 1.266 1188 METABOLITES_END #END