#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         	┬ÁM
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