OR example file: metabolomics

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Metadata Organism_sample Data_ExtracellularMetabolites Results_CalculatedFluxes Instrument_chemostat Instrument_measurements_envPara MediumComposition

Metadata	Values
Asset Title	Characterization of flux distribution and general physiology of S. pyogenes in continuous cultures
Uploader	Martijn Bekker
Uploader SEEK ID	53
Project	SysmoLab

ASSAY
Assay SEEK ID	109
Assay Title	Physiological characterization of Lactic acid bacteria grown in C-limited continuous cultures
Assay_type	catabolic flux distribution
Technology_type	HPLC
Description	S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15
Experimentalist	person 1, person 2
Date	2010-08-01T0:0:0+0000
SOP	2


Experimental_conditions
Item	temperature	Growth_Medium	Growth_Medium
Compound (if concentration)		Glucose	Acetate
Unit	ºC	mM	mM
Start_value (optional)		65	12
End_value (optional)	37
Comments		standard medium with additional glucose	standard medium with additional acetate
Culture Growth	Chemostat
FACTORS_STUDIED
Item	pH	dilution_rate
Compound (if concentration)
Unit		1/h
Start_value (optional)	6.5	0.05
End_value (optional)	7.5	0.15
SD (optional)
Comments		Growth rate dependent flux distribution

Treatment(s)

Sample

Chemostat

Organism

NCBI_ID

Strain

Genotype

Phenotype

organism/cell part

Dilution_rate

Culture_start_date

Date_at_sampling

Age_at_sampling_hours

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

wild-type

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

wild-type

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

wild-type

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

wild-type

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

Δldh

low ability for utilization of carbon source

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

Δldh

low ability for utilization of carbon source

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

Δldh

low ability for utilization of carbon source

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

Δldh

low ability for utilization of carbon source

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch134_37_pH_6

Streptococcus pyogenes

1314

M49

whole cell

0.15

2014-11-11T14:0:0+0000

2014-11-16T14:0:0+0000

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

11a

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

del ldh

low ability for utilization of carbon source

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

del ldh

low ability for utilization of carbon source

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

del ldh

low ability for utilization of carbon source

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

13a

ch137_35_pH_7

Streptococcus pyogenes

1314

M49

del ldh

low ability for utilization of carbon source

whole cell

0.05

2014-11-14T9:0:0+0000

2014-11-18T14:0:0+0000

ch143_37_pH6_5

Streptococcus pyogenes

1314

M49

wild type

whole cell

6.5

0.22

2014-11-22T8:0:0+0000

2014-11-26T14:0:0+0000

ch143_37_pH6_5

Streptococcus pyogenes

1314

M49

wild type

whole cell

6.5

0.22

2014-11-22T8:0:0+0000

2014-11-26T14:0:0+0000

ch143_37_pH6_5

Streptococcus pyogenes

1314

M49

delta ldh

low ability for utilization of carbon source

whole cell

6.5

0.22

2014-11-22T8:0:0+0000

2014-11-26T14:0:0+0000

ch143_37_pH6_5

Streptococcus pyogenes

1314

M49

delta ldh

low ability for utilization of carbon source

whole cell

6.5

0.22

2014-11-22T8:0:0+0000

2014-11-26T14:0:0+0000

Metabolite	Sample	Glucose	Ethanol	Acetate	Lactate	Formiate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	CO2
		mM		mM	nM	mM		nM	mM	mM
	1	3	19,3 mM	35.1	70	35.4	0,4 mM	1.5	0	0	0.06
	2	4	8,7 mM	20.3	99.7	8.1	0,4 mM	1.4	0	0	0.06
	3	3.5	11,3 mM	22.8	83.8	13.6	0,1 mM	0	0	0	0.06
	4	3	1,6 mM	20.2	56.2	20.7	0,4 mM	0	0	0	0.06
	5	4	1,6 mM	40.3	1.8	65.4	0,2 mM	8.2	3.2	0	0.06
	6	3.5	1,6 mM	42.1	2.3	74.6	0,4 mM	19.5	3	0	0.06
	7	3	1,6 mM	40.8	1.7	71.5	0,4 mM	15.4	2.6	0	0.06
	8	4	8,3 mM	39.6	0.8	69	0,4 mM	15	2.5	1	0.06
	9	3.5	11,3 mM	26.5911	33.2897	27.1529	0,4 mM	0.2222	9.0482	0	0.06
	10	3	11,3 mM	58.4248	12.1797	71.7257	0,6 mM	0.2573	2.9294	0	0.06
	11	4	1,3 mM	46.1068	34.7783	45.5907	0,4 mM	0	1.7379	0	0.06
	11a	3.5	7,3 mM	25.3673	65.3299	11.4123	0,4 mM	0	1.7817	0	0.06
	12	3	5,7 mM	0	0	0	0,4 mM	0	0	1.2	0.06
	13	4	1,3 mM	16.1389	85.2263	0	0,8 mM	0	1.0621	0	0.06
	13a	3.5	4,6 mM	35.0679	66.9688	26.5225	0,4 mM	0	1.6499	0	0.06
	14	3	0,1 mM	15.1085	96.3673	0	0,4 mM	0	1.178	0	0.06
	15	4	1,3 mM	32.5884	69.796	17.6214	0,4 mM	0.806	0	0	0.06
	16	3.5	12,3 mM	35.4929	75.7861	0	0,4 mM	0.4942	0	0	0.06
	17	3.5	07,3 mM	44.4907	68.0624	38.2789	0,4 mM	0	0	0	0.06

		Metabolite
Sample	Dilution rate	Glucose	Ethanol	Acetate	Lactate	Formate	Succinate	Pyruvate	Acetoin	2,3-butanediol
		CHEBI:17234	CHEBI:16236	CHEBI:30089	CHEBI:24996	CHEBI:15740	CHEBI:30779	CHEBI:15361	CHEBI:15688	CHEBI:62064
Unit	/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
1	0.05	-2.7083333333333335	0.8041666666666668	0.9625	2.916666666666667	1.475	0	0.06250000000000001	0	0
2	0.15	-13.928571428571429	0	1.778571428571429	21.364285714285717	1.7357142857142855	0	0.3	0	0
3	0.05	-5	0.6384615384615385	0.8307692307692308	6.446153846153846	1.0461538461538462	0	0	0	0
4	0.15	-9.75	1.65	1.2299999999999998	8.43	3.105	0	0	0	0
5	0.05	-3.25	2.205	1.415	0.09000000000000001	3.2700000000000005	0	0.41	0.16000000000000003	0
6	0.15	-7.8	6.684	3.6119999999999997	0.27599999999999997	8.952	0	2.34	0.36	0
7	0.05	-5	4.7	2.215384615384615	0.13076923076923078	5.5	0	1.1846153846153846	0.2	0
8	0.15	-9.285714285714285	7.8999999999999995	3.942857142857142	0.11428571428571428	9.857142857142856	0	2.142857142857143	0.35714285714285715	0
9	0.05	-4.887218045112782	2.150345864661654	1.0970751879699248	2.5029849624060154	2.0415714285714284	0.20536842105263156	0.016706766917293236	0.6803157894736841	0
10	0.05	-7.222222222222222	3.6155999999999997	5.158311111111111	1.3533000000000002	7.969522222222222	0.4703777777777778	0.028588888888888886	0.3254888888888889	0
11	0.05	-5.613636363636301	1.460486818181802	2.94558727272724	3.003580454545421	3.9373786363635928	0	0	0.15009136363636197	0
11a	0.15	-11.470588235294118	0.7946647058823529	2.358935294117647	11.52880588235294	2.013935294117647	0	0	0.3144176470588236	0
12	0.05	-7.386363636363637	0	-1.3636363636363638	0	0	0	0	0	0
13	0.15	-12.355397260273973	0	0.8504589041095889	17.512253424657533	0	0	0	0.21823972602739727	0
13a	0.05	-4.126984126984206	0.766501587301602	1.4646285714285996	4.251987301587382	1.6839682539682863	0	0	0.10475555555555754	0
14	0.15	-18.055555555555554	0	0.863472222222222	26.768694444444442	0	0	0	0.3272222222222222	0
15	0.05	-4.421768707482879	0.46373469387753913	1.4005714285713924	4.748027210884232	1.1987346938775203	0.01065306122448952	0.0548299319727877	0	0
16	0.05	-4.744525547445547	0	1.7148102189782075	5.531832116788662	0	0.04459124087591516	0.036072992700732144	0	0
17	0.15	-14.828897338402546	2.6066007604561863	7.4123269961974705	15.527543726235221	8.732828897338111	0.08009885931558669	0	0	0

	Sample	Date	Chemostat	Medium flow	Volume	Temperature	pH	Dilution rate	%O2 input	Airflow	N2 flow	Total flow	Comments
Unit	1	Date	name	ml/hour	ml	Celcius	1	1/hour	volume%	ml/min	ml/min	ml/min	1
	1	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	6.5	0.05	0	0	500	100	wild-type
	2	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	6.5	0.15	0	0	500	100	wild-type
	3	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	7.5	0.05	0	0	500	100	wild-type
	4	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	7.5	0.15	0	0	500	100	wild-type
	5	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	6.5	0.05	0	0	500	100	Δldh
	6	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	6.5	0.15	0	0	500	100	Δldh
	7	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	7.5	0.05	0	0	500	100	Δldh
	8	2014-11-11T14:0:0+0000	ch134_37_pH_low		750	37	7.5	0.15	0	0	500	100	Δldh
	9	2014-11-14T9:0:0+0000	ch137_35_pH_high	50	1000	37	6.5	0.05	0	0	100	100	wild-type
	10	2014-11-14T9:0:0+0000	ch137_35_pH_high	50	1000	37	7.5	0.05	0	0	100	100	wild-type, way to high OD
	11	2014-11-14T9:0:0+0000	ch137_35_pH_high	50	1000	37	7.5	0.05	0	0	100	100	wild-type
	11a	2014-11-14T9:0:0+0000	ch137_35_pH_high	75	500	37	7.5	0.15	0	0	100	100	wild-type
	12	2014-11-14T9:0:0+0000	SYSMO4	50	1000	37	7.5	0.05	0	0	100	100	wild-type
	13	2014-11-14T9:0:0+0000	SYSMO4	150	1000	37	7.5	0.15	0	0	100	100	wild-type
	13a	2014-11-14T9:0:0+0000	SYSMO3	50	1000	37	7.5	0.05	0	0	100	100	wild-type
	14	2014-11-14T9:0:0+0000	SYSMO4	150	1000	37	6.5	0.15	0	0	100	100	wild-type
	15	2014-11-14T9:0:0+0000	SYSMO3	50	1000	37	6.5	0.05	0	0	100	100	wild-type
	16	2014-11-14T9:0:0+0000	SYSMO4	50	1000	37	6.5	0.05	0	0	100	100	wild-type
	17	2014-11-14T9:0:0+0000	SYSMO4	150	1000	37	6.5	0.15	0	0	100	100	wild-type

Identifier	Sample	CO2	O2	CO2	pH	RPM	OD	standard deviation OD	Dryweight correction calculated	Dry weight	Dry weight	standard deviation dryweight
Unit		volume%	volume%	volume%	1	rpm	AU	AU		gram/liter	gram/liter	gram/liter
Description		Inputgas	Outputgas	Outputgas		stirring rate	Optical density (600nm)	Optical density (600nm)		Calculated	Dryweight measured as described in SOP X
	1					400	2.55		0.47058823529411764	0.85	1.2
	2					400	2.36		0.2966101694915254	0.7866666666666666	0.7
	3					400	2.22		0.2927927927927928	0.7400000000000001	0.65
	4					400	2.1		0.47619047619047616	0.7000000000000001	1
	5					400	2.27		0.44052863436123346	0.7566666666666667	1
	6					400	2.94		0.4251700680272109	0.98	1.25
	7					400	1.65		0.393939393939394	0.5499999999999999	0.65
	8					400	2.43		0.43209876543209874	0.81	1.05
	9	0.01	ND	ND	6.3	400	2.275	0.10606601717796739	0.2923076923076923	0.7583333333333333	0.665	0.24748737341529123
	10	0.01	ND	ND	7.41	400	5.4	0.14142135623729543	0.08333333333333333	1.8	0.45	0.08485281374238561
	11	0.01	ND	ND	7.21	400	2.29	0.1697056274847673	0.25281544472535333	0.7633333333333333	0.5789473684210591	0.029772917102586262
	11a	0.01	ND	ND	7.44	400	2.555	0.10606601717799251	0.33268101761252444	0.8516666666666667	0.85	0.0742462120246034
	12	0.01	ND	ND	7.51	400	1.31	0.15556349186103902	0.33587786259541985	0.4366666666666667	0.44	0.0742462120246034
	13	0.01	ND	ND	7.32	100	2.27	0.09899494936611793	0.32158590308370044	0.7566666666666667	0.73
	13a	0.01	ND	ND	ND	100	2.0666666666666664	0.09073771725877823	0.38104838709676697	0.6888888888888888	0.787499999999985	0.18031222920258855
	14	0.01	ND	ND	6.44	100	1.62	0.3676955262170038	0.3333333333333333	0.54	0.54
	15	0.01	ND	ND	6.46	100	2.203333333333333	0.15567059238448272		0.7344444444444443	0.735000000000019	0.07778174593052666
	16	0.01	ND	ND	6.57	100	1.8966666666666667	0.15044378795195365		0.6322222222222222	0.6849999999999579	0.014142135623761574
	17	0.01	ND	ND	6.69	100	1.38	0.20223748416156723		0.45999999999999996	0.657500000000022	0.003535533905865814

Identifier	Sample	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	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	2	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	3	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	4	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	5	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	6	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	7	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	8	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	9	65	0	12	0	0	0	0	0	0
	10	65	0	12	0	0	0	0	0	0
	11	65	0	12	0	0	0	0	0	0
	11a	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	12	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	13	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	13a	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	14	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	15	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	16	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	17	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	0	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	0	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	0	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	0	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	0	65	0	12	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0