#METABOLOMICS WORKBENCH araskind_20150606_9816311_mwtab.txt DATATRACK_ID:275 STUDY_ID:ST000178 ANALYSIS_ID:AN000275 PROJECT_ID:PR000153
VERSION             	1
CREATED_ON          	01-15-2019
#PROJECT
PR:PROJECT_TITLE                 	Graft-Versus-Host Disease
PR:PROJECT_SUMMARY               	T cell metabolism during graft-versus-host disease
PR:INSTITUTE                     	University of Michigan
PR:DEPARTMENT                    	Pediatrics
PR:LABORATORY                    	Ferrara lab
PR:LAST_NAME                     	Byersdorfer
PR:FIRST_NAME                    	Craig
PR:ADDRESS                       	Ann Arbor, MI
PR:EMAIL                         	craigbye@med.umich.edu
PR:PHONE                         	734-000-0000
PR:DOI                           	http://dx.doi.org/10.21228/M8B01C
#STUDY
ST:STUDY_TITLE                   	T cell metabolism during graft-versus-host disease (CAB 307)-PART I
ST:STUDY_TYPE                    	Glycolysis/TCA/Nucleotide analysis (tissue/cells)
ST:STUDY_SUMMARY                 	T cells were injected into mice to model graft-versus-host disease.  On day 7
ST:STUDY_SUMMARY                 	after bone marrow transplantation (BMT), cells were recovered and CD8 T cells
ST:STUDY_SUMMARY                 	were purified to > 90% purity over magnetic columns.  Naïve T cells were used
ST:STUDY_SUMMARY                 	as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with
ST:STUDY_SUMMARY                 	anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to
ST:STUDY_SUMMARY                 	BSA (in PBS).  Cells were incubated at 37oC for 60min, after which time they
ST:STUDY_SUMMARY                 	were removed from the plates, counted, and an equal number (2.5x10^6) were
ST:STUDY_SUMMARY                 	placed into a 1.7 ml micro-centrifuge tubes and spun down.  Cells were washed
ST:STUDY_SUMMARY                 	once with ammonium chloride, residual volume was removed by a second brief spin,
ST:STUDY_SUMMARY                 	cell pellets were flash frozen in liquid nitrogen and stored at -80oC until
ST:STUDY_SUMMARY                 	analysis. Several mice lines were used in this study.
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@umich.edu
ST:PHONE                         	-
#SUBJECT
SU:SUBJECT_TYPE                  	Animal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:SPECIES_GROUP                 	Mammal
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	SU0004282	S00015097	Treatment:Control	
SUBJECT_SAMPLE_FACTORS           	SU0004282	S00015098	Treatment:Control	
SUBJECT_SAMPLE_FACTORS           	SU0004282	S00015099	Treatment:Control	
SUBJECT_SAMPLE_FACTORS           	SU0004282	S00015100	Treatment:Control	
SUBJECT_SAMPLE_FACTORS           	SU0004281	S00015094	Treatment:GVHD	
SUBJECT_SAMPLE_FACTORS           	SU0004281	S00015095	Treatment:GVHD	
SUBJECT_SAMPLE_FACTORS           	SU0004281	S00015096	Treatment:GVHD	
#COLLECTION
CO:SAMPLE_TYPE                   	Cells
CO:COLLECTION_SUMMARY            	-
#TREATMENT
TR:TREATMENT_SUMMARY             	-
#SAMPLEPREP
SP:SAMPLEPREP_PROTOCOL_FILENAME  	Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx
SP:SAMPLEPREP_SUMMARY            	-
#CHROMATOGRAPHY
CH:METHODS_ID                    	AQM011
CH:METHODS_FILENAME              	ALPHA_KETO_ACIDS-FULL.M.zip
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   	ALPHA_KETO_ACIDS-FULL.M.zip
AN:PROCESSING_PARAMETERS_FILE    	EX00317-MassHunterQuant-GlyTCA-DataAnalysis-GCMS-Method.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         	pmol/µg protein
MS_METABOLITE_DATA_START
Samples	S00015097	S00015098	S00015099	S00015100	S00015094	S00015095	S00015096
Factors	Treatment:Control	Treatment:Control	Treatment:Control	Treatment:Control	Treatment:GVHD	Treatment:GVHD	Treatment:GVHD	
Alanine					1.1190	0.9812	1.4374
alpha-Ketoglutarate	0.6082	0.6201	0.6114	0.4602	0.4289	0.3928	0.4765
Aspartate	11.5010	12.0246	17.0131	8.5928	24.8296	24.0247	27.3494
fumarate	1.2111	1.2342	1.2184	0.9111	0.9026	0.8082	0.9775
Glutamate	0.9925	0.9029	0.8984	0.5906	1.8674	1.7041	2.1098
glutamine				2.2511	1.8603	1.8879	2.0947
Lactate		1.8413	1.5102		1.2362	2.8291	1.2722
Oxaloacetate							
pyruvate	3.0709	3.1656	3.1729	2.3696	2.4151	2.2261	2.8650
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	5950		C00041	ALA	UM_Target_ID				
alpha-Ketoglutarate	51		C00026	AKG	UM_Target_ID				
Aspartate	5960		C00049	ASP	UM_Target_ID				
fumarate	444972		C00122	FUM	UM_Target_ID				
Glutamate	611			GLU	UM_Target_ID				
glutamine	5961		C00064	GLN	UM_Target_ID				
Lactate	107689		C00186	LAC	UM_Target_ID				
Oxaloacetate	970		C00036	OAA	UM_Target_ID				
pyruvate	1060		C00022	PYR	UM_Target_ID				
METABOLITES_END
#END