#METABOLOMICS WORKBENCH huntermoseley_20190215_183041 DATATRACK_ID:1625 STUDY_ID:ST001139 ANALYSIS_ID:AN001869
VERSION                          	1
CREATED_ON                       	02-08-2024
#PROJECT
PR:PROJECT_TITLE                 	P4HA1 knockdown in the breast cell line MDA231
PR:PROJECT_SUMMARY               	Determine the effect of knocking down P4HA1 in the MDA231 cell line (including
PR:PROJECT_SUMMARY               	alterations to metabolic pathways).
PR:INSTITUTE                     	University of Kentucky
PR:DEPARTMENT                    	Markey Cancer Center
PR:LAST_NAME                     	Xu
PR:FIRST_NAME                    	Ren
PR:ADDRESS                       	BBSRC361, 741 South Limestone, Lexington, KY 40536, USA
PR:EMAIL                         	ren.xu2010@uky.edu
PR:PHONE                         	000-000-0000
PR:DOI                           	http://dx.doi.org/10.21228/M8T10P
#STUDY
ST:STUDY_TITLE                   	P4HA1 knockdown in the breast cell line MDA231 Gln metabolism (part VI)
ST:STUDY_TYPE                    	isotope tracer
ST:STUDY_SUMMARY                 	Determine the effect on glutamine metabolism of knocking down P4HA1 in the
ST:STUDY_SUMMARY                 	MDA231 cell line.
ST:INSTITUTE                     	University of Kentucky
ST:DEPARTMENT                    	Markey Cancer Center
ST:LAST_NAME                     	Xiong
ST:FIRST_NAME                    	Gaofeng
ST:ADDRESS                       	BBSRC361, 741 South Limestone, Lexington, KY 40536, USA
ST:EMAIL                         	gaofeng.xiong@uky.edu
ST:PHONE                         	000-000-0000
ST:SUBMIT_DATE                   	2019-02-15
#SUBJECT
SU:SUBJECT_TYPE                  	Animal
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A	protocol.id:13C15NGln_shCTL	lineage_1=2_MDA231_13C15NGln_shCTL_rep1; cell_type=MDA231; plate_with_media_weight=19.66; plate_with_media_weight%units=g; replicate=1; lineage_2=2_MDA231_13C15NGln_shCTL_rep1-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage2']; replicate=1; replicate%type=analytical; sample_split_ratio=0.28579888665166403; type=polar; weight=0.4825999999999999; weight%units=g; lineage_4=2_MDA231_13C15NGln_shCTL_rep1-cells-protein; dry_weight=0.0008000000000000229; dry_weight%units=g; protein_weight=0.5884; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
SUBJECT_SAMPLE_FACTORS           	-	3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A	protocol.id:13C15NGln_shCTL	lineage_1=3_MDA231_13C15NGln_shCTL_rep2; cell_type=MDA231; plate_with_media_weight=19.65; plate_with_media_weight%units=g; replicate=2; lineage_2=3_MDA231_13C15NGln_shCTL_rep2-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage3']; replicate=1; replicate%type=analytical; sample_split_ratio=0.25640876252621786; type=polar; weight=0.44010000000000016; weight%units=g; lineage_4=3_MDA231_13C15NGln_shCTL_rep2-cells-protein; dry_weight=0.0006999999999999229; dry_weight%units=g; protein_weight=0.5808; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
SUBJECT_SAMPLE_FACTORS           	-	4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A	protocol.id:13C15NGln_shCTL	lineage_1=4_MDA231_13C15NGln_shCTL_rep3; cell_type=MDA231; plate_with_media_weight=19.17; plate_with_media_weight%units=g; replicate=3; lineage_2=4_MDA231_13C15NGln_shCTL_rep3-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage4']; replicate=1; replicate%type=analytical; sample_split_ratio=0.2617664493183165; type=polar; weight=0.4416000000000002; weight%units=g; lineage_4=4_MDA231_13C15NGln_shCTL_rep3-cells-protein; dry_weight=0.0007000000000000339; dry_weight%units=g; protein_weight=0.5344000000000001; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
SUBJECT_SAMPLE_FACTORS           	-	6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A	protocol.id:13C15NGln_shP4HA1	lineage_1=6_MDA231_13C15NGln_shP4HA1_rep1; cell_type=MDA231; plate_with_media_weight=19.13; plate_with_media_weight%units=g; replicate=1; lineage_2=6_MDA231_13C15NGln_shP4HA1_rep1-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage6']; replicate=1; replicate%type=analytical; sample_split_ratio=0.2785457645697584; type=polar; weight=0.45740000000000025; weight%units=g; lineage_4=6_MDA231_13C15NGln_shP4HA1_rep1-cells-protein; dry_weight=0.0009000000000000119; dry_weight%units=g; protein_weight=0.5952000000000001; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
SUBJECT_SAMPLE_FACTORS           	-	7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A	protocol.id:13C15NGln_shP4HA1	lineage_1=7_MDA231_13C15NGln_shP4HA1_rep2; cell_type=MDA231; plate_with_media_weight=19.66; plate_with_media_weight%units=g; replicate=2; lineage_2=7_MDA231_13C15NGln_shP4HA1_rep2-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage7']; replicate=1; replicate%type=analytical; sample_split_ratio=0.2859185984148737; type=polar; weight=0.4797999999999998; weight%units=g; lineage_4=7_MDA231_13C15NGln_shP4HA1_rep2-cells-protein; dry_weight=0.0010999999999999899; dry_weight%units=g; protein_weight=0.5852; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
SUBJECT_SAMPLE_FACTORS           	-	8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A	protocol.id:13C15NGln_shP4HA1	lineage_1=8_MDA231_13C15NGln_shP4HA1_rep3; cell_type=MDA231; plate_with_media_weight=19.3; plate_with_media_weight%units=g; replicate=3; lineage_2=8_MDA231_13C15NGln_shP4HA1_rep3-cells; cell_type=MDA231; protocol.id=cell_quench_collection; lineage_3=8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A; protocol.id=['polar_extraction', 'NMR_file_storage8']; replicate=1; replicate%type=analytical; sample_split_ratio=0.2918280979912975; type=polar; weight=0.48960000000000004; weight%units=g; lineage_4=8_MDA231_13C15NGln_shP4HA1_rep3-cells-protein; dry_weight=0.0008999999999999009; dry_weight%units=g; protein_weight=0.6532; protein_weight%units=mg; protocol.id=protein_extraction; type=protein
#COLLECTION
CO:COLLECTION_SUMMARY            	Collection and quench of cells in culture
CO:COLLECTION_PROTOCOL_ID        	cell_quench_collection
CO:COLLECTION_PROTOCOL_FILENAME  	3A_Cells_Quench_Cell_Fan_20170412.pdf
CO:SAMPLE_TYPE                   	cultured cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Cells grown in unlabeled glutamine and infected with empty vector. Cells grown
TR:TREATMENT_SUMMARY             	in unlabeled glutamine and infected with shP4HA1 lentivirus. Cells grown in
TR:TREATMENT_SUMMARY             	labeled glutamine and infected with empty vector. Cells grown in labeled
TR:TREATMENT_SUMMARY             	glutamine and infected with shP4HA1 lentivirus.
TR:TREATMENT_PROTOCOL_ID         	12C14NGln_shCTL 12C14NGln_shP4HA1 13C15NGln_shCTL 13C15NGln_shP4HA1
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Polar extraction from cells. Protein extraction and quantification.
SP:SAMPLEPREP_PROTOCOL_ID        	polar_extraction protein_extraction
SP:SAMPLEPREP_PROTOCOL_FILENAME  	4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf;4D_17Jun4_Fan_Prot_Quant.pdf
#CHROMATOGRAPHY
#ANALYSIS
AN:ANALYSIS_TYPE                 	NMR
#NMR
NM:INSTRUMENT_NAME               	Agilent 600
NM:INSTRUMENT_TYPE               	FT-NMR
NM:NMR_EXPERIMENT_TYPE           	HC-HSQC
NM:STANDARD_CONCENTRATION        	0.5 mM
NM:SPECTROMETER_FREQUENCY        	600 MHz
NM:NMR_PROBE                     	cryogenic triple resonance HCN
NM:NMR_SOLVENT                   	D20
NM:NMR_TUBE_SIZE                 	1.7 mm
NM:SHIMMING_METHOD               	gradient shimming
NM:PULSE_SEQUENCE                	gHSQCAD
NM:WATER_SUPPRESSION             	presaturation
NM:CHEMICAL_SHIFT_REF_CPD        	DSS
NM:TEMPERATURE                   	15 celsius
NM:ACQUISITION_TIME              	2 s
NM:RELAXATION_DELAY              	4 s
NM:BASELINE_CORRECTION_METHOD    	Bernstein Polynomial
#NMR_METABOLITE_DATA
NMR_METABOLITE_DATA:UNITS        	Peak area normalized
NMR_METABOLITE_DATA_START
Samples	2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A	3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A	4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A	6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A	7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A	8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A
Factors	protocol.id:13C15NGln_shCTL	protocol.id:13C15NGln_shCTL	protocol.id:13C15NGln_shCTL	protocol.id:13C15NGln_shP4HA1	protocol.id:13C15NGln_shP4HA1	protocol.id:13C15NGln_shP4HA1	
Asp-3a_1	24.5423	29.7037	24.6903	30.2698	27.1926	39.0372
Asp-3a_2	31.1144		34.9874	35.4275	38.3173	18.8921
Asp-3b_1	16.0053	19.9233	17.7178	18.3136	26.2934	12.4482
Asp-3b_2	24.0222		20.4347	18.5852	21.5341	12.1033
DSS_1	3.7089	2.7599	3.5932	3.3434	2.8324	2.8002
Gln-3_1	228.3296	181.8510	245.8179	184.8079	182.7145	298.4413
Gln-3_2	201.0946		177.7722	304.1650	294.0866	
Gln-4_1	94.5777	51.5843	66.8797	75.2415	67.4374	106.0323
Gln-4_2	86.4081	53.6395	92.7602	84.8903	99.0015	88.7858
Gln+Glu-2_1	231.4167	200.0727	209.9923	175.1039	205.1693	197.4518
Glu-3-a_1	814.6414	592.3812	110.2269	700.7143	681.2972	116.9320
Glu-3-a_2	28.9067	16.8148	455.6918	7.3636		302.2954
Glu-3-a_3			30.3685			381.9717
Glu-3-a_4						36.1272
Glu-3-b_1	207.4967	622.2894	177.5475	258.9825	178.9555	278.1596
Glu-3-b_2	510.6707		342.3489	360.6655	451.9234	943.6137
Glu-4_1	261.1516	231.5831	221.2428	255.6909	231.9403	328.4375
GSH+GSSG-3_1	97.7528	183.3769	115.8869	89.3400	104.2341	44.2969
GSH+GSSG-3_2		65.8716				
GSH+GSSG-4_1	49.0177	35.5730	48.5555	53.6964	42.5425	42.1479
Lac-3_1	8.3287	4.6150	7.1817	8.2858	8.7615	10.2799
P-Cho A_1	10.9800	8.0427	9.5417	10.0932	9.2622	10.8910
NMR_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	pubchem_id	inchi_key	kegg_id	other_id	other_id_type	ri	ri_type	moverz_quant	
Asp-3a_1									
Asp-3a_2									
Asp-3b_1									
Asp-3b_2									
DSS_1									
Gln-3_1									
Gln-3_2									
Gln-4_1									
Gln-4_2									
Gln+Glu-2_1									
Glu-3-a_1									
Glu-3-a_2									
Glu-3-a_3									
Glu-3-a_4									
Glu-3-b_1									
Glu-3-b_2									
Glu-4_1									
GSH+GSSG-3_1									
GSH+GSSG-3_2									
GSH+GSSG-4_1									
Lac-3_1									
P-Cho A_1									
METABOLITES_END
#END