Growth-rate dependent catabolic flux disitribution

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Metadata Environmental parameters Measurements environ parameters Medium composition (measured) Extracellular metabolites Calculated fluxes

Item	Value
Experimentator	Martijn
Raw data
Reference	SYSMO-LAB

Description	Growth in glucose-limited chemostat conditions at low growth rates with slow increases in oxygenation
Aim	Effect of aeration of pyruvate branching
Strain information	NZ9000
Strain	Lactococcus lactis
Vessel type	Applikon fermentor
Stirring rate	400	RPM
Temperature	37	degree celcius
Dilution rate	factor studied	/h
Volume	1000	ml
Gas flow	500	ml
pH	6.5
SOP's used
Jermtype	1

Explanations	Format	Data

TOPIC
Titel	text	Carbon metabolism and its response to different dilutions rate in glucose-limited chemsotat conditions
Comments	text	some comments

ASSAY
Title	text	In vivo metabolites concentrations
Assay_type	integer	Catabolic flux distributions
Comments

EXPERIMENT
Experiment_description	text	chemostat 1
Experiment_type	text	time series
Experimentalist	text	Martijn Bekker

Begin_date	date	39619
User	integer	your name
Group	integer	your group
SOP		SOP 4




ORGANISM
Organism	integer	L. lactis
NCBI_ID	integer	7777777
Strain	text	NZ9000
Genotype	text	wild-type
Phenotype	text	wild-type
Culture_starting_date		varying
Date_at_sampling		varying
Age_at_sampling_hours	integration	varying


Experimental_conditions
Item	text	pH	temperature	buffer
Start_value	float/text	6.5	37	1
End_value	float/text	6.5	37
Unit	text	dimensionlesss	ºC
Comments


FACTORS_STUDIED
Item	text	Dilution rate
Start_value	float/text	0.15
End_value	float/text
Unit	text	per hour
Comments		Growth rate dependent flux distribution

DATA_CREATED
Datatype	text	External metabolite concentrations
Creation_date	date	39802
Status	text	row, normalised, ....
Person_created	text	Martijn Bekker

DATA_FILE
File_name	text	Chemostat dilution rates.xls
File_type	text	excel sheet
Storage_location	text	https://sysmolab.wikispaces.com/LacMetSS_DR
Storage_date	date	39803
Last_change_date	date	39817
TemplateID	text	Chemostat template

PUBLICATION
Title	text	1
Authors	text	1
Journal	text	1
URL	text	1
Year	text	1
Volume	text	1
Pages	text	1
PubmedID	text	1
UserID	text	1
GroupID	text	1
ProjectID	text	1
ExperimentID	text	1

	experiment run	measurementnumber	Age	Date	Chemostat	Medium flow	Volume	Temperature	pH Chemostat	Dilution rate	%O2 input	Airflow	N2 flow	Total flow	Comments
Unit	1	1	hours	Date	name	ml/hour	ml	Celcius	1	1/hour	volume%	ml/min	ml/min	ml/min	1
	1	1	72	2009-01-30T0:0:0+0000	Santostaat	15	100	37	6.5	0.15	0	0	100	100	Old chemostat, however looks good
	2	1	50	2009-02-05T0:0:0+0000	Santostaat	32	100	37	6.5	0.32	0	0	100	100	Looks good, little filaments
	3	1	50	2009-02-09T0:0:0+0000	Santostaat	32	100	37	6.5	0.32	0	0	100	100	Looks good, little filaments
	4	1	120	2009-02-25T0:0:0+0000	Santostaat	50	100	37	6.5	0.5	0	0	100	100	Looks good, little filaments
	5	1	96	2009-03-03T0:0:0+0000	Santostaat	50	100	37	6.5	0.5	0	0	100	100	Looks good, little filaments
	6	1	72	2009-03-12T0:0:0+0000	Santostaat	40	100	37	6.5	0.4	0	0	100	100	Looks good, no filaments att all
	7	1	30	2009-04-08T0:0:0+0000	Santostaat	26	100	37	6.5	0.26	0	0	100	100	Looks good, little filaments
	7	2	54	2009-04-09T0:0:0+0000	Santostaat	26	100	37	6.5	0.26	0	0	100	100	Looks good, little filaments
	8	1	120	2009-04-15T0:0:0+0000	Santostaat	11	100	37	6.5	0.11	0	0	100	100	Looks good, no filaments att all
	9	1	120	2009-04-01T0:0:0+0000	Santostaat	40	100	37	6.5	0.4	0	0	100	100	Looks good, no filaments att all

Identifier	experiment run	measurementnumber	O2	O2	CO2	pH	RPM	OD	standard deviation OD	Dry weight	standard deviation dryweight
Unit	1	1	volume%	volume%	volume%	1	rpm	AU	AU	gram/liter	gram/liter
Description			Inputgas	Outputgas	Outputgas		stirring rate	Optical density (600nm)	Optical density (600nm)	Dryweight measured as described in SOP X
	1	1				6.46	400			0.39
	2	1					400			0.7
	3	1					400	0.98		0.56	0.04
	4	1					400	1.47		0.36	0.1
	5	1					400	2.59		0.47	0.03
	6	1					400	2.26	0.18	0.63	0.06
	7	1					400			0.47	0.01
	7	2					400			0.46	0.03
	8	1					400			0.42	0.03
	9	1					400			0.42	0.07

Identifier	Experiment	measurementnumber	Glucose	Ethanol	Acetate	Lactate	Formiate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	%O2	CO2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine
Unit			mM	mM	mM	mM	mM	mM	mM	mM	mM	%	%	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	μM	mM	mM	mM	mM
	1	1	14.6327	0	11.2431	0	0	0	0	2.0329	0			1.978	2.476	10.417000000000002	0.416	2.2489999999999997	2.488	1.024	9.871	1.823	1.268	2.742	1.6059999999999999	0.2488	0.1024	0.9871	0.1823	0.1268	0.2742	0.1606
	2	1	14.6327	0	11.2431	0	0	0	0	2.0329	0			1.9100000000000001	2.949	2.0869999999999997	2.495	0.827	5.6610000000000005	2.113	1.695	1.6869999999999998	4.447	0	1.689	2.114	0.665	0	1.411	1.181	2.522	1.813
	3	1	12.6909	0	10.0972	0	0	0	0	1.9949	0			1.9100000000000001	2.949	2.0869999999999997	2.495	0.827	5.6610000000000005	2.113	1.695	1.6869999999999998	4.447	0	1.689	2.114	0.665	0	1.411	1.181	2.522	1.813
	4	1	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262
	5	1	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262			5.41	7.0969999999999995	6.475999999999999	3.975	1.84	11.303	5.968999999999999	3.363	4.25	8.919		2.271	4.626	1.3569999999999998	0	4.1370000000000005	2.127	5.157	3.1990000000000003
	6	1	29.7755	0	13.945	0	0	0	0	2.9134	0			5.41	7.0969999999999995	6.475999999999999	3.975	1.84	11.303	5.968999999999999	3.363	4.25	8.919		2.271	4.626	1.3569999999999998	0	4.1370000000000005	2.127	5.157	3.1990000000000003
	7	1	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262			6.211	4.444	7.83	2.596	1.782	19.813000000000002	3.1990000000000003	2.234	5.3069999999999995	11.06		2.404	4.898	1.289	4.484	4.389	1.786	4.973	3.16
	7	2	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262			6.211	4.444	7.83	2.596	1.782	19.813000000000002	3.1990000000000003	2.234	5.3069999999999995	11.06		2.404	4.898	1.289	4.484	4.389	1.786	4.973	3.16
	8	1	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262			6.211	4.444	7.83	2.596	1.782	19.813000000000002	3.1990000000000003	2.234	5.3069999999999995	11.06		2.404	4.898	1.289	4.484	4.389	1.786	4.973	3.16
	9	1	29.6492	0	13.9686	0	0	0	0	2.8399	0.3262			6.211	4.444	7.83	2.596	1.782	19.813000000000002	3.1990000000000003	2.234	5.3069999999999995	11.06		2.404	4.898	1.289	4.484	4.389	1.786	4.973	3.16

Identifier	Experiment	measurementnumber	Glucose	Ethanol	Acetate	Lactate	Formiate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	CO2	O2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine
Unit	1	1	mM	mM	mM	mM	mM	mM	mM	mM	mM	%	%	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	μM	mM	mM	mM	mM
	1	1	0	11.1	21.0082	5.7598	21.1087	0	0	0	0			3.384	1.4849999999999999	3.008	2.096	0.859	10.982000000000001	0	1.444	2.13	6.469	0.057999999999999996	1.814	2.3449999999999998	0.738	109.12599999999999	2.091	1.125	2.683	1.9389999999999998
	2	1	0	6.9177	15.2913	3.6368	15.0696	0	0	1.697	0			1.61	0.781	1.514	0.245	0.659	4.49	0	0.7	1.07	2.768	0	0.917	1.2089999999999999	0.294	43.855	0.898	0.545	1.29	1.0879999999999999
	3	1	0	6.0046	17.1202	6.0676	14.6716	0	0	1.7956	0			1.918	0.982	1.693	2.293	0.726	6.538	0	1.159	1.363	3.963	0	1.503	1.6789999999999998	0.533	51.123000000000005	1.097	0.795	1.905	1.609
	4	1	0	4.1226	17.1944	32.3732	10.0748	0.741	0.2275	2.4089	0													0
	5	1	0	3.6442	17.2144	35.9842	9.3864	0.7716	0.329	2.5304	0			0.5920000000000001	0.252	0.598	0.458	0.252	1.2770000000000001	0.055	0.235	0.40399999999999997	1.189	0	0.23800000000000002	0.41200000000000003	0.06799999999999999	11.783999999999999	0.21600000000000003	0.23099999999999998	0.449	0.27199999999999996
	6	1	0	2.7906	16.6124	39.2926	7.3411	0	0.3698	2.6364	0			6.1339999999999995	2.633	5.38	3.62	1.678	18.438000000000002	0.62	2.308	3.487	8.263	0	1.678	3.809	0.983	201.168	3.51	1.453	3.9429999999999996	2.65
	7	1	0	4.0374	16.6954	25.8455	9.6157	0	0.2449	2.0343	0			4.209	1.617	3.61	2.182	1.09	12.473	0	1.7280000000000002	2.4179999999999997	5.583	0	1.692	2.502	0.5369999999999999	120.441	2.042	0.974	2.605	1.6520000000000001
	7	2	0	3.1717	16.4636	29.7712	7.7778	0.8035	0.2717	2.6857	0			5.532	2.117	4.8420000000000005	2.886	1.494	16.082	0	2.384	3.245	7.2540000000000004	0	2.31	3.395	0.786	174.735	3.007	1.321	3.5970000000000004	2.314
	8	1	0	16.7097	30.275	7.6746	34.9087	0.9761	0.7749	2.3819	0
	9	1	0	2.25	16.39	31.56	6.45	0.79	0	2.11	0			3.495	1.434	3.252	1.859	0.937	9.216999999999999	0.588	1.34	2.065	4.819	0	1.365	2.184	0.47100000000000003	80.55199999999999	1.726	0.926	2.3169999999999997	1.391

Identifier	experiment run	measurementnumber	Dilution rate	Glucose	Ethanol	Acetate	Lactate	Formate	Succinate	Pyruvate	Acetoin	2,3-butanediol	CO2	O2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine	Yield glucose	Yield glucose	ATP (calculated)	Lactate (mol/mol glucose)	Formate (mol/mol glucose)
Unit	1	1	/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	g/mol	g/g	mmol/gram/hour	mol/mol	mol/mol
	1	1	0.15	-5.627961538461538	4.269230769230768	3.755807692307691	2.215307692307692	8.118730769230769	0	0	-0.7818846153846154	0	0	0	0.5407692307692307	-0.3811538461538462	-2.8496153846153853	0.6461538461538462	-0.5346153846153844	3.2669230769230775	-0.3938461538461538	-3.241153846153846	0.11807692307692304	2.000384615384615	-1.0323076923076924	0.08000000000000007	0.806230769230769	0.24446153846153842	0.04159188461538461	0.7341153846153847	0.3839230769230769	0.9264615384615383	0.6839999999999998	26.652634168677004	0.14807018982598336	12.432384615384612	0.3936252366275534	1.4425704073752625
	2	1	0.32	-6.689234285714287	3.162377142857143	1.8506057142857142	1.6625371428571432	6.88896	0	0	-0.15355428571428575	0	0	0	-0.13714285714285718	-0.9910857142857142	-0.26194285714285703	-1.0285714285714287	-0.07679999999999997	-0.5353142857142859	-0.9659428571428572	-0.4548571428571429	-0.2820571428571428	-0.7675428571428573	0	-0.35291428571428574	-0.41371428571428576	-0.16960000000000003	0.020048000000000003	-0.23451428571428573	-0.2907428571428572	-0.5631999999999999	-0.3314285714285715	47.838061328394616	0.2657670073799701	8.219017142857144	0.24853923062729366	1.0298577842776793
	3	1	0.32	-7.251942857142856	3.4311999999999996	4.0131428571428565	3.4671999999999996	8.383771428571428	0	0	-0.11388571428571417	0	0	0	0.004571428571428449	-1.1239999999999999	-0.22514285714285698	-0.1154285714285714	-0.0577142857142857	0.501142857142857	-1.2074285714285713	-0.3062857142857143	-0.18514285714285705	-0.2765714285714285	0	-0.10628571428571437	-0.24857142857142858	-0.07542857142857141	0.02921314285714286	-0.17942857142857144	-0.22057142857142856	-0.3525714285714284	-0.11657142857142855	44.12610610752588	0.24514503393069934	14.696914285714286	0.4781063596750428	1.1560724613699582
	4	1	0.5	-41.17944444444445	5.725833333333334	4.48027777777778	44.962777777777774	13.992777777777778	1.0291666666666668	0.31597222222222227	-0.5986111111111112	-0.45305555555555554	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12.141980222063326	0.06745544567812958	59.920138888888886	1.0918743170136123	0.33980006205901
	5	1	0.5	-31.541702127659576	3.8768085106382983	3.4529787234042564	38.281063829787236	9.985531914893617	0.8208510638297872	0.35000000000000003	-0.3292553191489361	-0.34702127659574467	0	0	-5.1255319148936165	-7.281914893617022	-6.2531914893617015	-3.741489361702128	-1.6893617021276597	-10.66595744680851	-6.291489361702128	-3.3276595744680852	-4.091489361702128	-8.22340425531915	0	-2.1627659574468083	-4.482978723404256	-1.3712765957446806	0.012536170212765957	-4.171276595744682	-2.0170212765957447	-5.008510638297873	-3.1138297872340432	15.852029734360455	0.08806683185755808	49.70297872340427	1.2136651241854755	0.3165818976565978
	6	1	0.4	-18.905079365079366	1.771809523809524	1.6935873015873022	24.94768253968254	4.661015873015873	0	0.23479365079365083	-0.175873015873016	0	0	0	0.4596825396825393	-2.834285714285714	-0.6958730158730153	-0.22539682539682537	-0.10285714285714297	4.530158730158732	-3.3961904761904758	-0.66984126984127	-0.4844444444444444	-0.4165079365079369	0	-0.3765079365079365	-0.5187301587301588	-0.23746031746031734	0.12772571428571428	-0.39809523809523856	-0.4279365079365078	-0.7707936507936511	-0.3485714285714288	21.15833487263018	0.11754630484794545	29.98971428571429	1.3196285536766803	0.24654833671978638
	7	1	0.26	-16.40168510638298	2.2334553191489364	1.508442553191489	14.297510638297876	5.319323404255321	0	0.13547659574468088	-0.4456510638297873	-0.18045106382978723	0	0	-1.1074893617021282	-1.563872340425532	-2.3344680851063835	-0.22902127659574478	-0.3828085106382979	-4.060425531914895	-1.7696595744680854	-0.2799148936170212	-1.5981702127659574	-3.0298297872340427	0	-0.39387234042553193	-1.3254468085106383	-0.41600000000000004	0.06414642553191491	-1.298340425531915	-0.4491914893617022	-1.3099574468085107	-0.834212765957447	15.852029734360455	0.08806683185755808	18.43112340425532	0.8717098606370494	0.3243156645035954
	7	2	0.26	-16.75824347826087	1.7927	1.4102173913043474	16.8272	4.396147826086956	0.45415217391304347	0.1535695652173913	-0.08715652173913038	-0.18437391304347825	0	0	-0.38378260869565234	-1.3152608695652173	-1.688869565217391	0.16391304347826088	-0.1627826086956522	-2.1088260869565225	-1.808130434782609	0.08478260869565213	-1.1654782608695649	-2.1512173913043475	0	-0.05313043478260862	-0.8495217391304345	-0.2843043478260869	0.09622882608695653	-0.7811304347826087	-0.26282608695652177	-0.7777391304347823	-0.4781739130434783	15.514752505969808	0.08619306947761005	21.959147826086955	1.004114782186366	0.2623274826976782
	8	1	0.11	-7.765266666666667	4.37635	4.270723809523808	2.010014285714286	9.142754761904763	0.2556452380952381	0.20295000000000002	-0.119952380952381	-0.08543333333333333	0	0	-1.6266904761904761	-1.163904761904762	-2.050714285714286	-0.679904761904762	-0.46671428571428575	-5.189119047619049	-0.8378333333333334	-0.5850952380952381	-1.3899285714285712	-2.896666666666667	0	-0.6296190476190476	-1.2828095238095236	-0.3375952380952381	-0.0011743809523809526	-1.1495000000000002	-0.46776190476190477	-1.3024523809523811	-0.8276190476190477	14.165643592407214	0.07869801995781786	15.23128095238095	0.2588467817006867	1.1773909582720614
	9	1	0.4	-28.237333333333336	2.142857142857143	2.306095238095238	30.05714285714286	6.142857142857143	0.7523809523809526	0	-0.6951428571428574	-0.3106666666666667	0	0	-2.586666666666667	-2.8666666666666667	-4.36	-0.701904761904762	-0.8047619047619049	-10.091428571428574	-2.4866666666666672	-0.8514285714285714	-3.0876190476190475	-5.9438095238095245	0	-0.9895238095238095	-2.584761904761905	-0.7790476190476189	0.0724457142857143	-2.5361904761904768	-0.8190476190476191	-2.5295238095238095	-1.6847619047619051	14.165643592407214	0.07869801995781786	36.30533333333334	1.064446932800885	0.21754381231196795