#METABOLOMICS WORKBENCH STUDY_ID:ST000282 ANALYSIS_ID:AN000450 PROJECT_ID:PR000224 VERSION 1 CREATED_ON 01-15-2019 #PROJECT PR:PROJECT_TITLE 13C mass isotopomer analysis PR:PROJECT_SUMMARY Pilot studies before designing future experiments PR:INSTITUTE University of Michigan PR:DEPARTMENT Internal Medicine PR:LABORATORY Merajver Lab PR:LAST_NAME Merajver PR:FIRST_NAME Sophia PR:ADDRESS University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105 PR:EMAIL smerajve@med.umich.edu PR:PHONE (734)936-6884 PR:DOI http://dx.doi.org/10.21228/M8K599 #STUDY ST:STUDY_TITLE Pilot Study 13C flux effects when RhoC or RhoA perturbed (13C BCs) ST:STUDY_TYPE 13C mass isotopomer analysis (flux studies) ST:STUDY_SUMMARY Rho-GTPases are small GTP-binding proteins that contribute to the ST:STUDY_SUMMARY epithelial-to-mesenchymal transition by regulating several cellular processes ST:STUDY_SUMMARY including organization of the actin cytoskeleton, cell motility, transcription, ST:STUDY_SUMMARY and cell proliferation. Overexpression of RhoC-GTPases (RhoC) in breast cancer ST:STUDY_SUMMARY has been implicated in poor disease prognosis due to increased cancer cells ST:STUDY_SUMMARY invasion, migration, and motility, which warranted its consideration as a ST:STUDY_SUMMARY therapeutic target for inhibiting breast cancer metastasis. Using silencing RNA ST:STUDY_SUMMARY (siRNA) molecules to knockdown RhoC expression is a promising approach to ST:STUDY_SUMMARY inhibit breast cancer metastases. ST:INSTITUTE University of Michigan ST:DEPARTMENT Internal Medicine ST:LABORATORY Merajver Lab ST:LAST_NAME Wynn ST:FIRST_NAME Michelle ST:ADDRESS University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105 ST:EMAIL mlwynn@umich.edu ST:PHONE 734-647-3408 #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 - S00017282 Cell line:MCF10A | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017283 Cell line:MCF10A | 13C Label:Glutamine | RhoC overexpression:yes | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017284 Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017287 Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes SUBJECT_SAMPLE_FACTORS - S00017286 Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017285 Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:yes | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017293 Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017295 Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017294 Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes SUBJECT_SAMPLE_FACTORS - S00017288 Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017290 Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017289 Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes SUBJECT_SAMPLE_FACTORS - S00017296 Cell line:SUM190 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017297 Cell line:SUM190 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017291 Cell line:SUM190 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no SUBJECT_SAMPLE_FACTORS - S00017292 Cell line:SUM190 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no #COLLECTION CO:SAMPLE_TYPE Cell Line CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_PROTOCOL_FILENAME Fluxomics_analysis_protocol-2015-03-11.docx SP:SAMPLEPREP_SUMMARY - #CHROMATOGRAPHY CH:METHODS_ID AQM012 CH:METHODS_FILENAME MAHMOUD-PALM_14ISOTOPE.M 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 MAHMOUD-PALM_14ISOTOPE.M.zip #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 Area normalized MS_METABOLITE_DATA_START Samples S00017282 S00017283 S00017284 S00017287 S00017286 S00017285 S00017293 S00017295 S00017294 S00017288 S00017290 S00017289 S00017296 S00017297 S00017291 S00017292 Factors Cell line:MCF10A | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:MCF10A | 13C Label:Glutamine | RhoC overexpression:yes | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no Cell line:MDA-MB-231 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:yes | RhoC knockdown:no | RhoC drug:no Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM149 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM149 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:yes Cell line:SUM190 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM190 | 13C Label:Glucose | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no Cell line:SUM190 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:no | RhoC drug:no Cell line:SUM190 | 13C Label:Glutamine | RhoC overexpression:no | RhoA knockdown:no | RhoC knockdown:yes | RhoC drug:no Alanine_123 37705.8280 23008.1325 8259.9317 2870.0593 13715.7836 8343.8267 16684.5733 13521.8592 25189.7417 14486.6003 22413.3150 44170.0969 4345.7377 4145.3034 12120.3625 6363.5129 Alanine_123_13C_1 89.0601 36.9355 63.3607 107.1542 139.4605 128.0320 26.0559 90.1874 Alanine_123_13C_2 Alanine_123_13C_3 alpha-Ketoglutarate_12345 1167.1053 856.9925 525.6054 55598.4662 437.5747 596.9446 514.9714 3845.1314 132.9317 166.2656 694.8123 2545.4614 1377.3865 5011.0314 alpha-Ketoglutarate_12345_13C_1 63.8209 57.3834 407.8694 230.3210 11.2907 54.0832 alpha-Ketoglutarate_12345_13C_2 61.9534 934.8282 25.7533 394.9057 382.9002 219.4731 alpha-Ketoglutarate_12345_13C_3 385.9749 9.5463 9.6259 7.9474 335.2523 2.4144 3.0198 146.4419 32.2709 111.6242 alpha-Ketoglutarate_12345_13C_4 0.5583 0.4648 152.5704 0.1412 0.1766 alpha-Ketoglutarate_12345_13C_5 1072.3978 555.6861 447.9348 668.4300 515.1836 127.4474 204.9378 255.3033 953.5011 570.8312 Aspartate_1234 21998.1872 18855.1682 7411.1952 3185.1291 41987.9867 5742.9868 28297.9313 20399.9517 18268.6043 6949.1039 9552.0866 2684.6593 445.2342 355.2057 663.7314 3585.5019 Aspartate_1234_13C_1 2461.5204 2310.9341 704.4278 95.3075 434.6223 584.7008 67.1045 2000.3499 827.9107 325.9885 185.5490 Aspartate_1234_13C_2 5107.0746 3593.9472 1049.9680 361.2513 706.4326 435.4320 1138.8715 766.7269 4638.7134 1782.9717 2696.6720 184.6711 120.1696 85.5184 Aspartate_1234_13C_3 1338.7011 1494.0540 278.6430 97.2518 627.2287 298.7381 1273.0059 652.8522 2778.6799 2668.8561 2614.1504 84.4704 35.5894 133.0126 Aspartate_1234_13C_4 12657.7071 9674.1397 2866.9316 770.6495 5928.3192 2640.6283 61.0813 798.1780 10311.6244 12994.4314 545.0884 540.1314 107.0179 Fumarate_1234 1221.3611 1109.8516 988.4868 1122.4661 57060.1845 992.8169 3446.9239 1247.6847 3479.6059 733.1242 2111.0734 1756.7977 4439.6823 2255.7269 3844.3945 18513.9520 Fumarate_1234_13C_1 69.4405 57.4688 23.9207 694.8476 158.1349 6.7867 173.0322 148.9513 39.3973 324.7744 544.2330 Fumarate_1234_13C_2 36.9502 6.9520 112.1124 417.4285 158.9015 184.7641 409.8655 326.0383 515.5010 418.0146 Fumarate_1234_13C_3 3.1573 118.8086 558.6137 377.1496 135.3201 407.0330 255.1261 596.3185 507.3710 Fumarate_1234_13C_4 148.2254 134.5831 982.7372 38.8048 1221.4167 393.4554 2200.3271 1265.3002 Glutamate_12345 58291.7126 42689.7636 25582.6539 12170.8064 66728.6139 16300.6179 112132.1513 71769.1121 132137.6235 16847.9120 23965.9184 31579.6749 5556.9560 4838.5505 4554.8558 8124.6163 Glutamate_12345_13C_1 5743.2364 5082.9382 1284.4415 531.1626 758.1975 1301.0345 323.9292 270.3392 5803.2445 908.1697 1393.0320 5113.9522 51.3408 366.8926 Glutamate_12345_13C_2 6253.0505 3893.5751 1374.7682 716.5965 685.3776 350.7001 6111.3318 3238.5265 38561.7316 1484.7695 1607.8413 4210.4630 542.7441 913.1260 345.2341 317.9575 Glutamate_12345_13C_3 20457.0481 13500.0837 5985.6890 2386.0507 6710.0983 4225.8809 443.8241 349.1018 10339.7205 6603.9926 9895.9251 10371.4997 161.3195 1050.4452 651.1181 Glutamate_12345_13C_4 3003.7339 1325.6300 1359.0518 535.3500 2665.7277 1197.8939 266.9975 10079.7459 2254.5583 3237.3825 2640.9949 88.0463 105.8990 246.4330 110.8685 Glutamate_12345_13C_5 63116.8469 37380.2206 24324.9224 8656.9296 55310.4649 27350.6669 177.7191 145.0226 3324.4157 47378.3564 72001.6792 58744.1438 77.3293 87.5044 4956.4944 2816.0482 Glutamine_12345 5777.7457 2816.6854 1393.8077 617.3679 12390.8140 1522.4285 32911.6977 27885.4966 10957.2094 1773.4625 2424.1092 889.7385 9537.4205 7586.4559 1220.8540 1272.0870 Glutamine_12345_13C_1 106.4938 452.1020 12.8496 251.1483 558.4941 11.6577 177.1869 22.3237 30.8955 Glutamine_12345_13C_2 23.1281 61.8149 225.8034 68.8998 101.3459 Glutamine_12345_13C_3 272.2480 0.4566 6.9830 638.6766 369.2625 270.1724 20.5457 896.5182 352.9787 10.4943 253.8185 Glutamine_12345_13C_4 337.0371 128.0303 11.0110 26.5208 68.2155 31.0253 14.9111 25.8982 Glutamine_12345_13C_5 56337.6739 28934.2028 18292.5280 4890.7948 46459.3117 20023.5934 20491.5762 35045.8051 10195.5116 16089.8831 10879.6690 Lactate_123 408863.9586 183156.6658 200641.2859 78977.8358 350046.4870 161002.0475 209876.8207 172655.4905 385925.9153 234246.7175 410127.2037 1894989.6870 102516.5115 88583.3450 282090.5989 186778.0069 Lactate_123_13C_1 620.2258 1571.4018 9677.8016 11077.3290 201.2440 146.0494 570.0420 Lactate_123_13C_2 3351.4775 1911.5341 2586.3961 2002.2677 2637.8429 2159.0850 6387.7520 4985.1745 50527.2140 1803.7365 2265.4261 6420.7333 3674.2826 3068.4780 2183.5737 722.2266 Lactate_123_13C_3 1908.4646 828.2198 866.6568 144.9773 393.0206 142064.1883 86536.0845 1547988.6020 859.8566 37.2925 12781.4279 65672.5666 40649.8578 1764.9994 698.6783 Oxaloacetate_1234 27752.2006 291598.4076 28805.8635 25372.4896 344265.3340 21002.3774 30844.7984 23169.5497 18007.3357 14448.3643 19965.4285 12488.8861 22741.9465 22342.5694 16171.7971 179636.0434 Oxaloacetate_1234_13C_1 865.7528 318.0047 33.5215 2226.0984 153.4814 177.0599 81.4193 81.9732 37.9963 Oxaloacetate_1234_13C_2 204.0038 5.0021 29.3414 Oxaloacetate_1234_13C_3 75.3821 29.9170 253.3663 97.1269 21.2233 59.3166 15.6676 Oxaloacetate_1234_13C_4 174.4873 69.9380 Pyruvate_123 65869.3045 48702.8835 82009.9887 2160.3368 168382.0789 78099.5577 54127.8827 42674.1907 40645.3267 79127.0494 99622.0356 14392.3044 29306.8431 35735.5218 5072.0908 49118.7127 Pyruvate_123_13C_1 227.4336 89.2907 170.9787 884.1199 96.0685 45.8206 33.0829 Pyruvate_123_13C_2 476.5580 147.8400 259.3862 1603.2524 1166.3572 4099.1396 261.5485 164.5814 3.8932 730.5522 628.3123 44.0305 54.9829 Pyruvate_123_13C_3 336.9688 187.7469 216.1213 128.9120 40787.7068 25184.2071 165930.5677 42.4644 12.5409 21106.8054 16659.9998 77.3582 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 Alanine_123 5950 C00041 ALA_123 UM_Target_ID Alanine_123_13C_1 5950 C00041 ALA_123_13C_1 UM_Target_ID Alanine_123_13C_2 5950 C00041 ALA_123_13C_2 UM_Target_ID Alanine_123_13C_3 5950 C00041 ALA_123_13C_3 UM_Target_ID alpha-Ketoglutarate_12345 51 C00026 AKG_12345 UM_Target_ID alpha-Ketoglutarate_12345_13C_1 51 C00026 AKG_12345_13C_1 UM_Target_ID alpha-Ketoglutarate_12345_13C_2 51 C00026 AKG_12345_13C_2 UM_Target_ID alpha-Ketoglutarate_12345_13C_3 51 C00026 AKG_12345_13C_3 UM_Target_ID alpha-Ketoglutarate_12345_13C_4 51 C00026 AKG_12345_13C_4 UM_Target_ID alpha-Ketoglutarate_12345_13C_5 51 C00026 AKG_12345_13C_5 UM_Target_ID Aspartate_1234 5960 C00049 ASP_1234 UM_Target_ID Aspartate_1234_13C_1 5960 C00049 ASP_1234_13C_1 UM_Target_ID Aspartate_1234_13C_2 5960 C00049 ASP_1234_13C_2 UM_Target_ID Aspartate_1234_13C_3 5960 C00049 ASP_1234_13C_3 UM_Target_ID Aspartate_1234_13C_4 5960 C00049 ASP_1234_13C_4 UM_Target_ID Fumarate_1234 444972 C00122 FUM_1234 UM_Target_ID Fumarate_1234_13C_1 444972 C00122 FUM_1234_13C_1 UM_Target_ID Fumarate_1234_13C_2 444972 C00122 FUM_1234_13C_2 UM_Target_ID Fumarate_1234_13C_3 444972 C00122 FUM_1234_13C_3 UM_Target_ID Fumarate_1234_13C_4 444972 C00122 FUM_1234_13C_4 UM_Target_ID Glutamate_12345 33032 GLU_12345 UM_Target_ID Glutamate_12345_13C_1 33032 GLU_12345_13C_1 UM_Target_ID Glutamate_12345_13C_2 33032 GLU_12345_13C_2 UM_Target_ID Glutamate_12345_13C_3 33032 GLU_12345_13C_3 UM_Target_ID Glutamate_12345_13C_4 33032 GLU_12345_13C_4 UM_Target_ID Glutamate_12345_13C_5 33032 GLU_12345_13C_5 UM_Target_ID Glutamine_12345 5961 C00064 GLN_12345 UM_Target_ID Glutamine_12345_13C_1 5961 C00064 GLN_12345_13C_1 UM_Target_ID Glutamine_12345_13C_2 5961 C00064 GLN_12345_13C_2 UM_Target_ID Glutamine_12345_13C_3 5961 C00064 GLN_12345_13C_3 UM_Target_ID Glutamine_12345_13C_4 5961 C00064 GLN_12345_13C_4 UM_Target_ID Glutamine_12345_13C_5 5961 C00064 GLN_12345_13C_5 UM_Target_ID Lactate_123 107689 C00186 LAC_123 UM_Target_ID Lactate_123_13C_1 107689 C00186 LAC_123_13C_1 UM_Target_ID Lactate_123_13C_2 107689 C00186 LAC_123_13C_2 UM_Target_ID Lactate_123_13C_3 107689 C00186 LAC_123_13C_3 UM_Target_ID Oxaloacetate_1234 970 C00036 OAA_1234 UM_Target_ID Oxaloacetate_1234_13C_1 970 C00036 OAA_1234_13C_1 UM_Target_ID Oxaloacetate_1234_13C_2 970 C00036 OAA_1234_13C_2 UM_Target_ID Oxaloacetate_1234_13C_3 970 C00036 OAA_1234_13C_3 UM_Target_ID Oxaloacetate_1234_13C_4 970 C00036 OAA_1234_13C_4 UM_Target_ID Pyruvate_123 1060 C00022 PYR_123 UM_Target_ID Pyruvate_123_13C_1 1060 C00022 PYR_123_13C_1 UM_Target_ID Pyruvate_123_13C_2 1060 C00022 PYR_123_13C_2 UM_Target_ID Pyruvate_123_13C_3 1060 C00022 PYR_123_13C_3 UM_Target_ID METABOLITES_END #END