#METABOLOMICS WORKBENCH araskind_20160112_9277591_mwtab.txt DATATRACK_ID:475 kenanazam_20160113_161707 STUDY_ID:ST000312 ANALYSIS_ID:AN000498 PROJECT_ID:PR000251
VERSION             	1
CREATED_ON             	January 13, 2016, 4:17 pm
#PROJECT
PR:PROJECT_TITLE                 	IDH1 gliomas
PR:PROJECT_SUMMARY               	Analyze IDH1R132H activity in glioma cell lines and tumnor tissue
PR:INSTITUTE                     	University of Michigan
PR:DEPARTMENT                    	Neurosurgery
PR:LABORATORY                    	Castro Lab
PR:LAST_NAME                     	Castro
PR:FIRST_NAME                    	Maria
PR:ADDRESS                       	Ann Arbor, MI
PR:EMAIL                         	mariacas@umich.edu
PR:PHONE                         	734-764-0850
#STUDY
ST:STUDY_TITLE                   	IDH1R132H activity in glioma cell lines and tumnor tissue (2HG)
ST:STUDY_TYPE                    	Regular
ST:STUDY_SUMMARY                 	We developed genetically engineered mice to generate brain tumors with especific
ST:STUDY_SUMMARY                 	genetic lessions. The animals were split in three groups: NRAS, P53 knockdown,
ST:STUDY_SUMMARY                 	IDH1-R132H and ATRX knock down (NPAID); NRAS, P53 knockdown, IDH1-R132H (NPI);
ST:STUDY_SUMMARY                 	NRAS, P53 knockdown, (NshP53). From these tumor we obtain and culture tumor
ST:STUDY_SUMMARY                 	cells growth like neurospheres and attached cells.
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                    	4
ST:TOTAL_SUBJECTS                	4
#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           	-	S00017646	Genetic makeup:NPAID	
SUBJECT_SAMPLE_FACTORS           	-	S00017647	Genetic makeup:NPI	
SUBJECT_SAMPLE_FACTORS           	-	S00017648	Genetic makeup:NshP53	
SUBJECT_SAMPLE_FACTORS           	-	S00020347	Genetic makeup:Pooled cells	
#COLLECTION
CO:COLLECTION_SUMMARY            	None provided.
CO:SAMPLE_TYPE                   	Cells
#TREATMENT
TR:TREATMENT_SUMMARY             	None provided.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	None provided.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	15DEC2015 2HG cells Castro.docx
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
MS:INSTRUMENT_NAME               	Agilent 6410A QQQ
CH:COLUMN_NAME                   	Waters Acquity HSS T3 (50 x 2.1mm, 1.8um)
CH:METHODS_FILENAME              	2015-04-07-2HG.m.zip
CH:METHODS_ID                    	DQM0033
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:MS_COMMENTS                   	-
MS:INSTRUMENT_NAME               	Agilent 6410A QQQ
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS         	µM/500µl extraction solvent
MS_METABOLITE_DATA_START
Samples	S00017646	S00017647	S00017648
Factors	Genetic makeup:NPAID	Genetic makeup:NPI	Genetic makeup:NshP53
D-2-hydroxyglutarate	10177.9815	3358.08205	2486.28377
L-2-hydroxyglutarate	182.37969	182.01126	454.50883
2-Phosphoglycerate/3-Phosphoglycerate	6.9806871	1.143851	4.5894202
6-phosphogluconic acid	37.638728	4.0799159	3.6714762
Acetyl-CoA	1.0653526	0.5927918	0.5995497
Adenosine diphosphate	33.130553	40.394093	41.9677
Adenosine monophosphate	153.44076	28.144997	44.537019
Adenosine triphosphate	11.329268	60.98457	67.54665
Citrate/iso-citrate	39.284676	7.8404032	3.760665
Fructose-6-Phosphate/glucose-6-phosphate	8.5134921	8.0508339	9.8884122
Flavin adenine dinucleotide	1.3357146	0.9016864	0.7557498
Fructose 1,6 Bisphosphate	40.714398	83.385701	182.38143
Malate	51.030168	16.612637	9.7442914
Nicotinamide adenine dinucleotide_1	0.6017222	0.076668	0.1132844
Nicotinamide adenine dinucleotide, reduced			
Nicotinamide adenine dinucleotide phosphate	0.9081965	0.80392	0.6518834
Nicotinamide adenine dinucleotide phosphate, reduced			
Phosphoenolpyruvate	0.8181748	0.5428246	1.0626774
D-ribulose-5-phosphate/D-xylulose-5-phosphate	41.767487	9.6581304	12.04663
Sedoheptulose-7P	128.23932	31.777984	31.560467
Succinate	50.19386	4.2907129	1.698174
Nicotinic acid			
Nicotinamide adenine dinucleotide_2	0.4297534	0.1688857	0.2019378
Nicotinamide	5.6608956	20.430295	9.5880366
Nicotinic acid mononucleotide	0.1541794	0.155716	0.1544609
Nicotinamide mononucleotide	0.1721849	0.1247026	0.1338116
Quinolinic acid	0.1506504	0.1303641	0.1301834
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	retention index	quantified m/z	PubChem ID	KEGG ID
D-2-hydroxyglutarate			439391	
L-2-hydroxyglutarate			439939	
2-Phosphoglycerate/3-Phosphoglycerate			724	
6-phosphogluconic acid			91493	
Acetyl-CoA			444493	
Adenosine diphosphate			6022	
Adenosine monophosphate			6083	
Adenosine triphosphate			5957	
Citrate/iso-citrate			311	
Fructose-6-Phosphate/glucose-6-phosphate			5958	
Flavin adenine dinucleotide			46906035	
Fructose 1,6 Bisphosphate			21125049	
Malate			525	
Nicotinamide adenine dinucleotide_1			15938971	
Nicotinamide adenine dinucleotide, reduced			439153	
Nicotinamide adenine dinucleotide phosphate			15938972	
Nicotinamide adenine dinucleotide phosphate, reduced			22833512	
Phosphoenolpyruvate			1005	
D-ribulose-5-phosphate/D-xylulose-5-phosphate			77982	
Sedoheptulose-7P			165007	
Succinate			1110	
Nicotinic acid			938	
Nicotinamide adenine dinucleotide_2			439153	
Nicotinamide			936	
Nicotinic acid mononucleotide			941	
Nicotinamide mononucleotide			14180	
Quinolinic acid			1066	
METABOLITES_END
#END