#METABOLOMICS WORKBENCH uchimiya_20240626_125357 DATATRACK_ID:4958 STUDY_ID:ST003304 ANALYSIS_ID:AN005414 PROJECT_ID:PR002054
VERSION             	1
CREATED_ON             	July 5, 2024, 6:46 am
#PROJECT
PR:PROJECT_TITLE                 	PyINETA: Open-source platform for INADEQUATE-JRES integration in NMR
PR:PROJECT_TITLE                 	metabolomics
PR:PROJECT_SUMMARY               	This study developed a new data analysis tool for metabolomics to integrate
PR:PROJECT_SUMMARY               	information of NMR experiments INADEQUATE and JRES. This deposition is for
PR:PROJECT_SUMMARY               	samples used for the validation of this new tool. Three mice were fed with a
PR:PROJECT_SUMMARY               	13C-labeled diet and the distribution of 13C-labeled metabolites was examined
PR:PROJECT_SUMMARY               	using INADEQUATE and JRES.
PR:INSTITUTE                     	University of Georgia
PR:LABORATORY                    	Edison Lab
PR:LAST_NAME                     	Mario
PR:FIRST_NAME                    	Uchimiya
PR:ADDRESS                       	315 Riverbend Rd, Athens, GA 30602
PR:EMAIL                         	mario.uchimiya@uga.edu
PR:PHONE                         	706-542-8387
PR:FUNDING_SOURCE                	NSF (1946970 awarded to A.S.E.); NIH (5R35GM148240 awarded to A.S.E.); The Max
PR:FUNDING_SOURCE                	Planck Society (awarded to C.W.T.)
PR:CONTRIBUTORS                  	Arthur S. Edison
#STUDY
ST:STUDY_TITLE                   	PyINETA: Open-source platform for INADEQUATE-JRES integration in NMR
ST:STUDY_TITLE                   	metabolomics
ST:STUDY_SUMMARY                 	This study developed a new data analysis tool for metabolomics to integrate
ST:STUDY_SUMMARY                 	information of NMR experiments INADEQUATE and JRES. This deposition is for
ST:STUDY_SUMMARY                 	samples used for the validation of this new tool. Three mice were fed with a
ST:STUDY_SUMMARY                 	13C-labeled diet and the distribution of 13C-labeled metabolites was examined
ST:STUDY_SUMMARY                 	using INADEQUATE and JRES.
ST:INSTITUTE                     	University of Georgia
ST:LAST_NAME                     	Mario
ST:FIRST_NAME                    	Uchimiya
ST:ADDRESS                       	315 Riverbend Rd, Athens, GA 30602
ST:EMAIL                         	mario.uchimiya@uga.edu
ST:PHONE                         	706-542-8387
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	1	Sample source:Liver | Factor_1 (tissue_type):1	RAW_FILE_NAME(Raw file name)=1; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	2	Sample source:Liver | Factor_1 (tissue_type):1	RAW_FILE_NAME(Raw file name)=2; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	3	Sample source:Brain | Factor_1 (tissue_type):2	RAW_FILE_NAME(Raw file name)=3; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	4	Sample source:Brain | Factor_1 (tissue_type):2	RAW_FILE_NAME(Raw file name)=4; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	6	Sample source:Brain | Factor_1 (tissue_type):2	RAW_FILE_NAME(Raw file name)=6; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	7	Sample source:Muscle | Factor_1 (tissue_type):3	RAW_FILE_NAME(Raw file name)=7; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	8	Sample source:Muscle | Factor_1 (tissue_type):3	RAW_FILE_NAME(Raw file name)=8; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	9	Sample source:Muscle | Factor_1 (tissue_type):3	RAW_FILE_NAME(Raw file name)=9; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	10	Sample source:Spleen | Factor_1 (tissue_type):4	RAW_FILE_NAME(Raw file name)=10; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	11	Sample source:Spleen | Factor_1 (tissue_type):4	RAW_FILE_NAME(Raw file name)=11; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	12	Sample source:Lung | Factor_1 (tissue_type):5	RAW_FILE_NAME(Raw file name)=12; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	13	Sample source:Lung | Factor_1 (tissue_type):5	RAW_FILE_NAME(Raw file name)=13; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	14	Sample source:Thymmus | Factor_1 (tissue_type):6	RAW_FILE_NAME(Raw file name)=14; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	15	Sample source:Thymmus | Factor_1 (tissue_type):6	RAW_FILE_NAME(Raw file name)=15; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	16	Sample source:Pancreas | Factor_1 (tissue_type):7	RAW_FILE_NAME(Raw file name)=16; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	17	Sample source:Pancreas | Factor_1 (tissue_type):7	RAW_FILE_NAME(Raw file name)=17; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	18	Sample source:Adrenal gland | Factor_1 (tissue_type):8	RAW_FILE_NAME(Raw file name)=18; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	19	Sample source:Adrenal gland | Factor_1 (tissue_type):8	RAW_FILE_NAME(Raw file name)=19; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	20	Sample source:Plasma | Factor_1 (tissue_type):9	RAW_FILE_NAME(Raw file name)=20; Biological replicate=2
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	21	Sample source:Plasma | Factor_1 (tissue_type):9	RAW_FILE_NAME(Raw file name)=21; Biological replicate=1
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	23	Sample source:Thymmus | Factor_1 (tissue_type):6	RAW_FILE_NAME(Raw file name)=23; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	24	Sample source:Pancreas | Factor_1 (tissue_type):7	RAW_FILE_NAME(Raw file name)=24; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	25	Sample source:Lung | Factor_1 (tissue_type):5	RAW_FILE_NAME(Raw file name)=25; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	26	Sample source:Plasma | Factor_1 (tissue_type):9	RAW_FILE_NAME(Raw file name)=26; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	27	Sample source:Spleen | Factor_1 (tissue_type):4	RAW_FILE_NAME(Raw file name)=27; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	29	Sample source:Adrenal gland | Factor_1 (tissue_type):8	RAW_FILE_NAME(Raw file name)=29; Biological replicate=3
SUBJECT_SAMPLE_FACTORS           	PyINETA testing	30	Sample source:Liver | Factor_1 (tissue_type):1	RAW_FILE_NAME(Raw file name)=30; Biological replicate=3
#COLLECTION
CO:COLLECTION_SUMMARY            	Liver, brain, thymus, lung, spleen, adrenal gland, pancrease, muscle, and plasma
CO:COLLECTION_SUMMARY            	samples were collected from three mice.
CO:COLLECTION_PROTOCOL_ID        	2_Collection protocol_UGA_PyINETA_2024.docx
CO:COLLECTION_PROTOCOL_FILENAME  	2_Collection protocol_UGA_PyINETA_2024.docx
CO:SAMPLE_TYPE                   	Whole animals
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	Three mice were fed with a diet that contains 13C labeled protein hydrolysate.
TR:TREATMENT_SUMMARY             	Details about the diet and 13C protein hydrolysate are indicated in the attached
TR:TREATMENT_SUMMARY             	file.
TR:TREATMENT_PROTOCOL_ID         	3_Treatment protocol_UGA_PyINETA_2024.docx
TR:TREATMENT_PROTOCOL_FILENAME   	3_Treatment protocol_UGA_PyINETA_2024.docx
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Tissue samples were homogenized and dried. Dried samples were resuspended in 50
SP:SAMPLEPREP_SUMMARY            	µL of deuterated water and methanol (1:4 volume ratio). The amount of material
SP:SAMPLEPREP_SUMMARY            	used is indicated in the attached file.
SP:SAMPLEPREP_PROTOCOL_ID        	4_Sample preparation protocol_UGA_PyINETA_2024.docx
SP:SAMPLEPREP_PROTOCOL_FILENAME  	4_Sample preparation protocol_UGA_PyINETA_2024.docx
SP:EXTRACT_STORAGE               	-80℃
#ANALYSIS
AN:DATA_FORMAT                   	ser
#NMR
NM:INSTRUMENT_NAME               	Bruker AVANCE lll
NM:INSTRUMENT_TYPE               	FT-NMR
NM:NMR_EXPERIMENT_TYPE           	Other
NM:NMR_COMMENTS                  	This data set is based on 13C-JRES. The original Bruker ser files for individual
NM:NMR_COMMENTS                  	13C-JRES specta are in folder 'Spectra'. Further details are also in the
NM:NMR_COMMENTS                  	attached protocol file.
NM:SPECTROMETER_FREQUENCY        	900
NM:NMR_PROBE                     	5-mm TXO cryoprobe
NM:NMR_TUBE_SIZE                 	1.7
#NMR_METABOLITE_DATA
NMR_METABOLITE_DATA:UNITS	NMR intensity (autoscaled)
NMR_METABOLITE_DATA_START
Samples	1	10	11	12	13	14	15	16	17	18	19	2	20	21	23	24	25	26	27	29	3	30	4	6	7	8	9
Factors	Sample source:Liver | Factor_1 (tissue_type):1	Sample source:Spleen | Factor_1 (tissue_type):4	Sample source:Spleen | Factor_1 (tissue_type):4	Sample source:Lung | Factor_1 (tissue_type):5	Sample source:Lung | Factor_1 (tissue_type):5	Sample source:Thymmus | Factor_1 (tissue_type):6	Sample source:Thymmus | Factor_1 (tissue_type):6	Sample source:Pancreas | Factor_1 (tissue_type):7	Sample source:Pancreas | Factor_1 (tissue_type):7	Sample source:Adrenal gland | Factor_1 (tissue_type):8	Sample source:Adrenal gland | Factor_1 (tissue_type):8	Sample source:Liver | Factor_1 (tissue_type):1	Sample source:Plasma | Factor_1 (tissue_type):9	Sample source:Plasma | Factor_1 (tissue_type):9	Sample source:Thymmus | Factor_1 (tissue_type):6	Sample source:Pancreas | Factor_1 (tissue_type):7	Sample source:Lung | Factor_1 (tissue_type):5	Sample source:Plasma | Factor_1 (tissue_type):9	Sample source:Spleen | Factor_1 (tissue_type):4	Sample source:Adrenal gland | Factor_1 (tissue_type):8	Sample source:Brain | Factor_1 (tissue_type):2	Sample source:Liver | Factor_1 (tissue_type):1	Sample source:Brain | Factor_1 (tissue_type):2	Sample source:Brain | Factor_1 (tissue_type):2	Sample source:Muscle | Factor_1 (tissue_type):3	Sample source:Muscle | Factor_1 (tissue_type):3	Sample source:Muscle | Factor_1 (tissue_type):3
Isoleucine	2.901533625	0.344826626	0.616301618	-0.400541878	-0.507604807	-0.453948137	-0.561032637	-0.162652298	-0.547805542	-0.380849683	-0.482031688	2.747299326	-0.462200886	-0.399605102	-0.186371496	-0.540604497	-0.548548806	-0.346165876	-0.289872545	-0.452458598	-0.414589773	2.342731124	-0.375388994	-0.563799166	-0.282279675	-0.066193749	-0.528146489
Alanine	2.726353517	0.065084293	0.001197138	0.041295268	-0.285050893	-0.559096229	-0.465265068	-0.204612799	0.606942211	-0.639302607	-0.635961518	3.437369591	-0.634323946	-0.611416479	-0.511633297	0.173006865	-0.401856327	-0.646302848	-0.055133868	-0.646546209	-0.629745088	1.37635339	-0.328886179	-0.559078426	-0.176468147	-0.270524955	-0.166397391
Valine	2.520145283	0.377723415	0.675045825	-0.340399505	-0.209211096	-0.61214614	-0.515640606	0.235749574	0.507252466	-0.678042193	-0.694989103	2.722083439	-0.714998759	-0.649893	-0.600893718	1.010846036	-0.635790371	-0.401724465	0.052962028	-0.7227166	-0.671948285	2.058882459	-0.539369981	-0.61071931	-0.575307428	-0.441936943	-0.544963022
Threonine	2.270413932	1.21527843	2.3417843	0.172323439	0.20055054	-0.819387736	-0.48482563	-0.517566753	0.137649058	-1.000562197	-0.955129301	1.252495181	-0.9378731	-0.793840114	-0.92857849	0.201121384	-0.645905892	-0.841496286	0.753337127	-0.925008113	-0.661509227	1.821428029	0.212044327	-0.221802312	-0.163345531	-0.527545045	-0.154050018
Lactic acid	2.630655912	0.228241045	0.031562689	-0.306512438	-0.586300774	-0.528355044	-0.54229931	-0.794017347	-0.648285082	-0.776263107	-0.781115127	2.845905778	-0.391370057	-0.608420739	-0.502335888	-0.778872083	-0.623572412	-0.429973979	-0.371174042	-0.719627258	-0.041263487	0.13603258	2.030017054	0.626893107	0.657903188	0.271048643	-0.02850182
Lysine	2.799751136	-0.69216184	0.158214597	-0.504462303	-0.080071453	-0.33497711	-0.536337123	-0.330710673	-0.486973725	-0.653464988	-0.606378761	3.385049457	-0.802475193	0.152336364	0.368507241	-0.833377119	1.012565086	-0.508768829	-0.187397841	-0.347287872	-0.491739064	0.740160145	-0.573515366	0.246913172	-0.224847029	-0.280362045	-0.388188866
Glutamine	1.616536134	-0.247502616	-0.245343944	-0.128936709	-0.316541864	-0.469815267	-0.402315934	-0.4682474	-0.270917143	-0.483627128	-0.485624604	4.234344906	-0.487864403	-0.49033694	-0.473509497	-0.449938504	-0.408041705	-0.482532344	-0.411488918	-0.471211509	-0.04205663	0.659188774	1.248233383	0.355443934	-0.275191568	-0.304426823	-0.298275682
Hypotaurine	-0.083432184	-0.391325514	-0.390608445	0.312076011	-0.112382042	-0.360926437	-0.241175627	2.463800484	3.676398177	-0.414163425	-0.451553368	0.196038646	-0.428340325	-0.424905504	-0.496592677	1.69384534	-0.456343122	-0.396652694	-0.47960403	-0.435179345	-0.442988412	-0.297811645	-0.419714533	-0.336572647	-0.400424527	-0.419815154	-0.461647003
Glutamic acid	3.155724559	-0.244812107	-0.284244727	-0.285290607	-0.301430785	-0.306785973	-0.297206621	-0.287672841	-0.257298659	-0.192847886	-0.287102431	3.756571206	-0.31379496	-0.279005168	-0.228347335	-0.285779695	-0.304028835	-0.271235589	-0.292769538	-0.277561675	-0.299241126	-0.288354588	-0.278479055	-0.285547329	-0.265834563	-0.263399364	-0.234224307
Taurine	2.580064765	0.573785019	1.094107517	0.729895951	0.369179995	-0.639899576	-0.381689051	-0.701676158	-0.601313995	-0.89185946	-0.866418223	2.948257627	-0.962913237	-0.964798768	-0.202474484	-0.656786248	-0.185908838	-0.969002506	0.166884317	-0.888892629	-0.668723955	0.874167176	0.119059544	-0.140949945	0.206890095	-0.179899754	0.240914821
O-phosphorylethanlamine	-0.51262428	1.807333916	2.558114956	0.060861165	0.042693027	-0.287628376	0.49744003	1.132425566	1.781085524	-0.779865019	-0.766367368	-0.245434034	-0.825191572	-0.69211922	0.407856468	1.668158726	-0.368347027	-0.796306373	0.949355644	-0.822472152	-0.788706112	-0.597587639	-0.438465313	-0.607116443	-0.794079172	-0.774560129	-0.808454795
Ethanolamine	0.895907489	2.077976352	1.711615513	1.060678185	0.365801387	-0.626306008	-0.749694074	-0.734403877	-0.626080272	-0.191891867	-0.554066023	3.212645219	-0.328974491	-0.560147573	-0.599552133	-0.243080915	-0.345541516	-0.654086478	-0.363005032	-0.409835474	-0.841913425	0.77559784	-0.547302362	-0.619125017	-0.535407646	-0.212012029	-0.357795773
D-glucuronate	3.614907564	-0.418288238	-0.418254383	-0.329907577	-0.037854396	-0.37889177	-0.399457978	-0.39748132	-0.429952328	-0.389643131	-0.403321145	2.298182551	0.059785748	-0.083065119	-0.422957277	-0.415643614	-0.392195893	0.193765353	-0.413160399	-0.405369718	-0.410497249	2.072754491	-0.4118515	-0.423199811	-0.431127079	-0.418290865	-0.408984917
NMR_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	BMRB_entry
Isoleucine	bmse000041
Alanine	bmse000028
Valine	bmse000052
Threonine	bmse000049
Lactic acid	bmse000208
Lysine	bmse000043
Glutamine	bmse000038
Hypotaurine	bmse000452
Glutamic acid	bmse000037
Taurine	bmse000120
O-phosphorylethanlamine	bmse000308
Ethanolamine	bmse000276
D-glucuronate	bmse000440
METABOLITES_END
#END