#METABOLOMICS WORKBENCH kenanazam_20160912_151130_mwtab.txt DATATRACK_ID:737 STUDY_ID:ST000469 ANALYSIS_ID:AN000733 PROJECT_ID:PR000360
VERSION             	1
CREATED_ON             	September 12, 2016, 3:23 pm
PR:PROJECT_TITLE                 	Enterococcus faecalis nucleotie profiles
PR:PROJECT_SUMMARY               	Determination of metabolite profiles of E. faecalis strains OG1RF (WT) and
PR:PROJECT_SUMMARY               	rel/relQ (ppGpp0)
PR:INSTITUTE                     	Univeristy of Florida
PR:DEPARTMENT                    	Oral Biology
PR:LABORATORY                    	Oral Biology Lemos-Abranches
PR:LAST_NAME                     	Lemos
PR:FIRST_NAME                    	Jose
PR:ADDRESS                       	1395 Center Drive, PO Box 100424 Gainesville, FL 32610
PR:EMAIL                         	jlemos@dental.ufl.edu
PR:PHONE                         	352-273-8843
PR:FUNDING_SOURCE                	UF start-up funds
ST:STUDY_TITLE                   	Enterococcus faecalis nucleotide profiles - pilot
ST:STUDY_TYPE                    	Comparison between wild-type and mutant strain, as well as providing varying
ST:STUDY_TYPE                    	cell count input for WT
ST:STUDY_SUMMARY                 	E. faecalis OG1RF and rel/relQ will be grown in FMC-AUG to OD600 = 0.25. 3E10
ST:STUDY_SUMMARY                 	cells will be harvested by fast filtration, scraped off of membrane into
ST:STUDY_SUMMARY                 	ice-cold PBS, and pelleted by centrifugation. This process will be repeated with
ST:STUDY_SUMMARY                 	OG1RF only to harvest 3E9 and 3E8 cells. A second OG1RF sample of 3E10 cells
ST:STUDY_SUMMARY                 	will be scraped into formic acid; only acid-soluble extract willl be sent for
ST:STUDY_SUMMARY                 	this sample.
ST:INSTITUTE                     	Univeristy of Florida
ST:DEPARTMENT                    	SECIM
ST:LABORATORY                    	Lemos-Abranches
ST:LAST_NAME                     	Kajfasz
ST:FIRST_NAME                    	Jessica
ST:ADDRESS                       	1395 Center Drive, PO Box 100424 Gainesville, FL 32610
ST:EMAIL                         	jkajfasz@dental.ufl.edu
ST:PHONE                         	352-273-6675
ST:NUM_GROUPS                    	5
ST:TOTAL_SUBJECTS                	5
SU:SUBJECT_TYPE                  	Bacterial cells
SU:SUBJECT_SPECIES               	Enterococcus faecalis
SU:TAXONOMY_ID                   	1351
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	Lemos_001	OG1RF_3E10	Strain:WT | Resuspension:PBS	CFU=3.00E+10
SUBJECT_SAMPLE_FACTORS           	Lemos_002	OG1RF_3E9	Strain:WT | Resuspension:PBS	CFU=3.00E+09
SUBJECT_SAMPLE_FACTORS           	Lemos_003	OG1RF_3E8	Strain:WT | Resuspension:PBS	CFU=3.00E+08
SUBJECT_SAMPLE_FACTORS           	Lemos_004	rel/relQ_3E10	Strain:(p)ppGpp0 | Resuspension:PBS	CFU=3.00E+10
SUBJECT_SAMPLE_FACTORS           	Lemos_005	OG1RF_3E10_acid	Strain:WT | Resuspension:1M Formic Acid	CFU=3.00E+10
CO:COLLECTION_SUMMARY            	3E9, 3E10 - upon reaching OD600 = 0.25, 100mL (OG1RF) or 425mL (rel/relQ) will
CO:COLLECTION_SUMMARY            	be harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will
CO:COLLECTION_SUMMARY            	be scraped off of the membrane into ice-cold PBS or formic acid (~1 mL),
CO:COLLECTION_SUMMARY            	centrifuged for 45 seconds at 12K RPM, liquid aspirated and stored at -80C until
CO:COLLECTION_SUMMARY            	sending for analysis.|3E8 - (OG1RF only). Upon reaching OD600 = 0.25, 1mL
CO:COLLECTION_SUMMARY            	culture will be harvested by 45 seconds centrifugation at 12K RPM, liquid
CO:COLLECTION_SUMMARY            	decanted, and stored at -80C until sending for analysis.
CO:SAMPLE_TYPE                   	Bacterial cells
TR:TREATMENT_SUMMARY             	This pilot study involves no treatment - cells will be grown in chemically
TR:TREATMENT_SUMMARY             	defined medium to an OD600 of 0.25 and harvested for analysis
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity
CH:COLUMN_NAME                   	Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)
CH:METHODS_FILENAME              	SB_NADH_Assay_Agilent.pdf
AN:ANALYSIS_TYPE                 	MS
MS:INSTRUMENT_NAME               	Agilent 6490 QQQ
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	NADH
MS_METABOLITE_DATA:UNITS         	nmol/mg protein
Samples	OG1RF_3E10	OG1RF_3E9	OG1RF_3E8	rel/relQ_3E10	OG1RF_3E10_acid
Factors	Strain:WT | Resuspension:PBS	Strain:WT | Resuspension:PBS	Strain:WT | Resuspension:PBS	Strain:(p)ppGpp0 | Resuspension:PBS	Strain:WT | Resuspension:1M Formic Acid
AMP	0.845457492			0.255958742	0.377771343
ADP	2.377354704	2.260149639	5.589016127	1.694243851	3.516579009
ATP	4.654067744	5.208946868		6.989888429	1.025161287
GDP	0.760383757	0.739643642		0.419042181	0.562394336
GTP	1.286746555	1.413418092		2.632834242	0.218756027
CDP	0.382224859	0.31849744		0.411867	0.655777432
CTP	0.988035124	1.219911451	1.078961586	2.477695127	0.323393839
UDP	0.87831059	0.779262793	1.349374202	0.590703813	1.10056381
UTP	3.223402275	3.796559869	3.217282727	4.902149993	0.763308277
metabolite_name	retention index	quantified m/z	PubChem ID	KEGG ID
AMP	1.51	348.1	6083
ADP	1.51	428	6022
ATP	1.5	508.1	5957
GDP	2.71	444.1	8977
GTP	2.78	524	6830
CDP	1.65	404.1	6132
CTP	1.67	484	6176
UDP	1.72	405	6031
UTP	1.79	485	6133