#METABOLOMICS WORKBENCH  STUDY_ID:ST000273 ANALYSIS_ID:AN000436
VERSION             	1
CREATED_ON          	01-03-2020
#PROJECT
PR:PROJECT_TITLE    	Longitudinal Studies of HIV-Associated Bacterial Pneumonia
PR:PROJECT_SUMMARY  	SCFA metabolites,  increased Treg, reduced Th17 lymphocytes and blunted immune
PR:PROJECT_SUMMARY  	response ex vivo
PR:INSTITUTE        	New York University
PR:DEPARTMENT       	Pulmonary Medicine
PR:LABORATORY       	Weiden Lab
PR:LAST_NAME        	Weiden
PR:FIRST_NAME       	Michael
PR:ADDRESS          	New York
PR:EMAIL            	michael.weiden@nyumc.org
PR:PHONE            	212-263-6479
PR:DOI              	http://dx.doi.org/10.21228/M8BP4D
#STUDY
ST:STUDY_TITLE      	Short-chain fatty acid analysis in bronchoalveolar lavage fluid (BAL SCFA)
ST:STUDY_TYPE       	We will correlate the bacterial gene abundance with the metabolite concentration
ST:STUDY_SUMMARY    	The study is intended to find if correlation exists between the abundance of
ST:STUDY_SUMMARY    	bacterial gene for pyruvate ferredoxin oxidoreductase (PFOR) and short-chain
ST:STUDY_SUMMARY    	fatty acids concentration in bronchoalveolar lavage fluid from patients with
ST:STUDY_SUMMARY    	HIV-Associated Bacterial Pneumonia.
ST:INSTITUTE        	University of Michigan
ST:DEPARTMENT       	Pulmonary Medicine(New York University School of Medicine)
ST:LABORATORY       	Weiden Lab(New York University School of Medicine)
ST:LAST_NAME        	Weiden
ST:FIRST_NAME       	Michael
ST:ADDRESS          	New York
ST:EMAIL            	michael.weiden@nyumc.org
ST:PHONE            	212-263-6479
ST:SUBMIT_DATE      	2014-03-26
ST:NUM_GROUPS       	2
ST:TOTAL_SUBJECTS   	39
ST:STUDY_COMMENTS   	PFOR stands for pyruvate ferredoxin oxidoreductase gene
#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           	-	S00013188	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013189	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013190	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013191	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013192	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013193	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013194	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013195	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013196	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013197	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013198	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013199	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013200	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013201	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013202	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013203	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013204	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013205	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013206	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013207	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013208	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013209	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013210	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013211	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013212	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013213	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013214	PFOR level:High	
SUBJECT_SAMPLE_FACTORS           	-	S00013176	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013177	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013178	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013179	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013180	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013181	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013182	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013183	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013184	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013185	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013186	PFOR level:Low	
SUBJECT_SAMPLE_FACTORS           	-	S00013187	PFOR level:Low	
#COLLECTION
CO:SAMPLE_TYPE                   	Bronchoalveolar Lavage Fluid
#TREATMENT
#SAMPLEPREP
SP:SAMPLEPREP_PROTOCOL_FILENAME  	SCFA_analysis_protocol-2015-03-10.docx
#CHROMATOGRAPHY
CH:METHODS_ID                    	AQM030
CH:METHODS_FILENAME              	WAXPLUS_100-200C_2_SIM.M.txt
CH:COLUMN_NAME                   	Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
CH:CHROMATOGRAPHY_TYPE           	GC
#ANALYSIS
AN:LABORATORY_NAME               	MRC2 (University of Michigan)
AN:ANALYSIS_TYPE                 	MS
AN:ACQUISITION_ID                	AQM030
AN:ACQUISITION_PARAMETERS_FILE   	WAXPLUS_100-200C_2_SIM.M.txt
AN:INSTRUMENT_NAME               	Agilent 7890A GC / 5975C MS
AN:PROCESSING_PARAMETERS_FILE    	EX00259-SCFA-Quant-methods.m.zip
AN:ANALYSIS_DISPLAY              	GCMS positive ion mode
AN:NUM_FACTORS                   	2
AN:NUM_METABOLITES               	7
#MS
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	
MS_METABOLITE_DATA_START
Samples	S00013188	S00013189	S00013190	S00013191	S00013192	S00013193	S00013194	S00013195	S00013196	S00013197	S00013198	S00013199	S00013200	S00013201	S00013202	S00013203	S00013204	S00013205	S00013206	S00013207	S00013208	S00013209	S00013210	S00013211	S00013212	S00013213	S00013214	S00013176	S00013177	S00013178	S00013179	S00013180	S00013181	S00013182	S00013183	S00013184	S00013185	S00013186	S00013187
Factors	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:High	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	PFOR level:Low	
aceticacid	125.4738	202.6652	16206.0356	90.1038	245.1341	52585.6805	404.1562	739.8899	576.9240	434.1006	815.4372	833.2870	946.3980	213577.3137	1034.0521	394.5271	298.3528	317.4493	305.2079	219.1145	34219.4352	484.0812	324.6209	326.7996	446.6337	1288.7821	418.4188	272.6739	108.4775	199.2590	187.7172	97.1326	81.4415	236.0357	663.1666	584.3792	1024.1801	586.6075	447.2441
butyricacid			173.2336			233.7818								240.5708							103.0454																		
heptanoicacid																																							
hexanoicacid	19.1643	19.0814	8.6892	19.7569	19.6920	9.8974	19.0185	37.0153	22.6553	18.1592	18.8641	22.8974	18.9476	10.0745	18.8856	21.9440	18.4657	19.3458	20.1644	20.1798	8.7564	21.1553	19.5101	19.0610	19.0768	38.3618	19.0822	38.7537	18.5654	23.6713	18.0812	18.9229	18.9418	21.9028	37.5680	35.2073	53.6142	36.6472	38.3886
isovalericacid	51.9048	51.9048	114.8345	52.4538	51.9048	147.2040	51.9048	103.8096	51.9048	52.5725	51.9048	52.0477	51.9048	143.1684	51.9048	51.9048	51.9048	51.9048	52.1758	52.1801	99.1897	52.1195	55.1237	51.9048	51.9048	104.4914	51.9048	105.4568	52.4877	55.8633	51.9048	52.2259	51.9048	51.9048	103.8096	103.8096	150.9958	104.1911	103.8096
propionic acid			165.9091			258.2328					6.4202	3.5826	10.7804	312.7194	11.0727						134.0618				0.6731	11.3477													
valericacid			57.5868			84.5696								86.2615							37.9877
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	
aceticacid	176		C00033	Acetate	UM_Target_ID				
butyricacid	20975673		C00246	Butyrate	UM_Target_ID				
heptanoicacid	8094		C05799	Heptanoate	UM_Target_ID				
hexanoicacid	8892		C01585	Hexanoate	UM_Target_ID				
isovalericacid	10430		C08262	Isovalerate	UM_Target_ID				
propionic acid	1032		C00163	Propionate	UM_Target_ID				
valericacid	7991		C00803	Valerate	UM_Target_ID				
METABOLITES_END