#METABOLOMICS WORKBENCH araskind_20160112_9711661_mwtab.txt DATATRACK_ID:476 kenanazam_20160113_164456 STUDY_ID:ST000313 ANALYSIS_ID:AN000499 PROJECT_ID:PR000252 VERSION 1 CREATED_ON January 13, 2016, 4:44 pm #PROJECT PR:PROJECT_TITLE Muscle Clock knock out metabolic changes PR:PROJECT_SUMMARY Inducible KO of Bmal1 in skeletal muscle; we see transcriptional changes PR:PROJECT_SUMMARY suggesting significant effects in TCA/substrate metabolism PR:INSTITUTE University of Kentucky PR:DEPARTMENT Physiology PR:LABORATORY Esser Lab PR:LAST_NAME Esser PR:FIRST_NAME Karyn PR:ADDRESS Lexington, KY PR:EMAIL karyn.esser@uky.edu PR:PHONE 859-323-8107 #STUDY ST:STUDY_TITLE Muscle Clock knock out mice metabolic changes (iMSBmal1-Exp1) ST:STUDY_TYPE Regular ST:STUDY_SUMMARY My lab studies the function of the molecular clocks in skeletal muscle. We have ST:STUDY_SUMMARY an inducible genetic mouse model (C57Bl6 background) in which we knock out the ST:STUDY_SUMMARY core clock gene, Bmal1, only in adult skeletal muscle after treatment with ST:STUDY_SUMMARY tamoxifen. We have found that the mice maintain body mass but lose fat mass at ST:STUDY_SUMMARY 10 weeks after loss of Bmal1. We have done expression profiling on the skeletal ST:STUDY_SUMMARY muscles and gene expression changes (insulin signaling, CHO metabolism, fat ST:STUDY_SUMMARY metabolism) suggest significant changes in substrate metabolism. To analyze TCA, ST:STUDY_SUMMARY CHO metabolites we have collected gastrocnemius muscles from these mice ST:STUDY_SUMMARY following instructions from Dr. Burant. Mice were anaesthetized with isoflurane, ST:STUDY_SUMMARY the gastrocnemius muscle dissected and flash frozen with tongs cooled with ST:STUDY_SUMMARY liquid N2. They have been stored in cryovials in our -80 freezer for 2 months. ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research 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 2 ST:TOTAL_SUBJECTS 14 #SUBJECT SU:SUBJECT_TYPE Animal 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 SU0012034 S00017942 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012035 S00017943 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012036 S00017944 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012037 S00017945 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012038 S00017946 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012039 S00017947 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012040 S00017948 muscle Bmal1:Bmal1 positive SUBJECT_SAMPLE_FACTORS SU0012041 S00017949 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012042 S00017950 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012043 S00017951 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012044 S00017952 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012045 S00017953 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012046 S00017954 muscle Bmal1:Bmal1 negative SUBJECT_SAMPLE_FACTORS SU0012047 S00017955 muscle Bmal1:Bmal1 negative #COLLECTION CO:COLLECTION_SUMMARY None CO:SAMPLE_TYPE Muscle, Skeletal #TREATMENT TR:TREATMENT_SUMMARY None #SAMPLEPREP SP:SAMPLEPREP_SUMMARY None SP:SAMPLEPREP_PROTOCOL_FILENAME Glycolysis-TCA-nucleotides-20150324.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm_bottompheater.m.zip #ANALYSIS AN:ANALYSIS_TYPE MS #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 S00017942 S00017943 S00017944 S00017945 S00017946 S00017947 S00017948 S00017949 S00017950 S00017951 S00017952 S00017953 S00017954 S00017955 Factors muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 positive muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative muscle Bmal1:Bmal1 negative 2 or 3-phosphoglycerate 2.478 3.434 3.054 2.490 0.427 4.708 2.153 0.992 0.435 1.144 0.449 0.725 3.069 1.650 6-phosphogluconate 0.061 0.058 0.066 0.064 0.047 0.021 0.021 0.034 0.042 0.047 0.034 0.035 0.097 0.055 acetyl-coa 0.007 0.005 0.003 0.001 0.007 0.001 0.001 0.007 0.005 0.003 0.002 0.002 0.009 0.005 adenosine diphosphate 3.319 3.311 1.703 3.763 2.918 2.187 2.623 2.792 2.744 2.384 3.105 2.850 1.857 2.605 Alpha-ketoglutaric acid 1.401 1.643 1.267 1.185 1.130 1.499 1.144 1.280 1.314 1.118 1.196 0.907 1.263 adenosine monophosphate 0.962 0.285 0.110 1.290 1.339 0.131 0.161 1.242 0.472 0.713 0.343 1.525 0.224 0.361 adenosine triphosphate 25.769 30.191 0.336 3.276 0.470 0.287 0.312 0.523 0.401 0.773 0.589 0.486 0.372 0.700 citrate or isocitrate 14.002 14.052 14.253 14.059 14.102 14.285 13.781 14.223 14.198 14.193 14.155 14.199 14.055 14.107 erythrose 4-phosphate 11.323 16.833 3.172 7.087 1.624 5.362 2.727 3.496 6.013 3.859 4.240 16.382 42.583 14.758 flavin adenine dinucleotide 0.152 0.164 0.174 0.099 0.141 0.175 0.169 0.203 0.179 0.160 0.148 0.151 0.162 0.157 fructose 1,6-bisphosphate 14.762 25.258 1.515 5.872 0.802 2.876 0.573 0.788 1.186 1.232 1.759 0.809 6.992 2.763 Fumaric acid 2.341 3.544 3.875 0.781 4.243 5.323 4.613 3.584 4.814 3.447 3.168 4.143 0.819 2.759 glucose 6-phosphate or fructose-6-phosphate 4.261 26.200 4.857 9.328 2.051 8.309 1.172 4.887 9.950 4.536 3.479 24.521 79.082 23.610 malate 5.604 6.244 6.617 6.528 7.596 8.942 9.771 7.650 8.614 6.655 6.159 7.666 9.289 8.712 nicotinamide adenine dinucleotide oxidized 2.600 2.471 0.196 1.332 0.553 0.111 0.236 0.345 0.214 0.709 0.233 0.369 0.098 0.315 nicotinamide adenine dinucleotide reduced 1.522 0.763 0.195 0.984 0.390 0.124 0.062 0.274 0.169 0.517 0.130 0.150 0.078 0.169 nicotinamide adenine dinucleotide phosphate oxidized 0.084 0.089 0.021 0.059 0.039 0.015 0.024 0.035 0.030 0.052 0.026 0.034 0.022 0.036 phosphoenolpyruvate 0.564 1.307 3.076 0.397 0.061 3.256 1.462 0.368 0.141 0.315 0.155 0.249 1.663 0.563 Pyruvic acid 46.614 44.378 35.248 33.822 37.484 79.523 47.247 38.126 46.909 126.092 62.834 43.445 ribose-5-phosphate or xylulose 5-phosphate 0.602 0.652 4.182 1.834 3.873 3.979 4.246 3.524 5.167 2.778 3.921 3.175 4.366 4.607 sedoheptulose 7-phosphate 0.064 0.050 0.025 0.034 0.043 0.020 0.037 0.020 0.111 0.032 0.037 0.092 0.170 0.065 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name retention index quantified m/z PubChem ID KEGG ID 2 or 3-phosphoglycerate 724 6-phosphogluconate 91493 acetyl-coa 444493 adenosine diphosphate 6022 Alpha-ketoglutaric acid 51 adenosine monophosphate 6083 adenosine triphosphate 5957 citrate or isocitrate 311 erythrose 4-phosphate 122357 flavin adenine dinucleotide 46906035 fructose 1,6-bisphosphate 21125049 Fumaric acid 444972 glucose 6-phosphate or fructose-6-phosphate 5958 malate 525 nicotinamide adenine dinucleotide oxidized 15938971 nicotinamide adenine dinucleotide reduced 439153 nicotinamide adenine dinucleotide phosphate oxidized 15938972 phosphoenolpyruvate 1005 Pyruvic acid 1060 ribose-5-phosphate or xylulose 5-phosphate 77982 sedoheptulose 7-phosphate 165007 METABOLITES_END #END