Absolute intracellular concentrations of metabolites extracted from T. b. brucei 427 wild type

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metadata samples Absolute concentrations Sheet3

Metadata	Values (examples)		Notes

Asset Title	Absolute concentration_fin2		The name of the data file
Uploader	Dong-Hyun Kim		The person submitting the asset to SEEK
Uploader SEEK ID	360		If you add your own SEEK ID, this will help us link this asset with your profile
Project	SilicoTryp		The project that the asset belongs to

ASSAY
Assay SEEK ID			If referring to an exisitng Assay, you can link to it via the Assay SEEK ID.
Assay Title			The title of an exisitng assay
Assay_type			The assay_type describes the type of experiment you are performing
Technology_type			Describes the type of instruments and/or equipment used for the experiment
Description			A brief, human readable description.
Experimentalist	Dong-Hyun Kim		The names of the people who carried out the experiments. These can either be SEEK members or external scientists
Date			The start date for the experiment if different from the upload date
SOP (protocol)	Generation of uniformly 13C-labelled E. coli extract for absolute quantification		Links to SOPs and protocols used to carry out the experiment. If they are already in SEEK, you can refer to them by their SEEK ID
SOP Type
Publication (optional)			If this data appears in a publication, you can link it directly, or via the assay or study. If it is already registered in SEEK, you can use the PubMed ID or DOI as a reference.

Experimental_conditions
Item	ExperimentalConditions	ExperimentalConditions	The name of the experimental condition you are fixing in your experiment (e.g. temperature, concentration, pH etc). If there is more than 1, please list them in columns across the spreadsheet
Compound (if concentration)			The compound name is only required if the item is concentration.
Unit			The SI units of the experimental conditions measurements.
Start_value (optional)			This field is used for recording changes throughout the experiment to measure different conditions (e.g. pH or dilutions)
End_value (optional)			This field is used for recording changes throughout the experiment to measure different conditions (e.g. pH or dilutions)
Comments			Additional information that would be useful for people reading this data file
Culture Growth	CultureGrowth

FACTORS_STUDIED
Item	FactorsStudied	FactorsStudied	Factors Studied are the factors that you deliberately change during the course of your experiment to see the effects. For example, if you measure the concentration of compounds at pH 5, 6 & 7, the factor studied is the pH (i.e. it is about the treatment you apply rather than the measurements you make).
Compound (if concentration)			The compound name is only required if the Factors Studied item is concentration.
Unit			The SI units of the factors studied measurements
Start_value (optional)			This field is used for recording changes throughout the experiment for one particular factor studied (e.g. pH in crease from 4 - 7 or dilution rate doubling)
End_value (optional)			This field is used for recording changes throughout the experiment for one particular factor studied (e.g. pH in crease from 4 - 7 or dilution rate doubling)
SD (optional)			The standard deviation for the difference in factors studied measurements (optional)
Comments			Additional information that would be useful for people reading this data file

Sample Name

Treatments (Factors Studied)

Culture_start_date

Date_at_sampling

Age_at_sampling_hours

Organism

NCBI_ID

Strain

Genotype

Phenotype

organism/cell part

e.g temperature

e.g Growth medium

date

age

Description

CM2

Trypanosoma_brucei

427 wild type

2×106 cells/ml in HMI9 medium supplemented with 10% FBS

CM4

Trypanosoma_brucei

427 wild type

4×106 cells/ml in HMI9 medium supplemented with 10% FBS

Note: this sheet allows you to describe your samples in as much detail as required. Sample names can be used in the data matrix file to relate different conditions to different experimental measurements


Name	Intracellular concentration (µM ± STE)
	CM2	CM4
(R)-2-Hydroxyglutarate	123.08±3.86	55.17±3.17
(S)-Malate	310.85±34.68	839.13±71.50
2-Oxoglutarate	809.48±33.57a	331.31±45.64
3-Methyl-2-oxobutanoic acid	82.85±7.19	130.13±13.24
3-Phospho-D-Glycerate	2154.85±58.12	1847.19±95.54
4-Aminobutanoate	18.59±1.74	6.40±1.01
5'-Methylthioadenosine	1.99±0.16	2.58±0.14
Adenine	1.07±0.10	1.80±0.45
Adenosine	26.97±2.15	43.20±16.13a
AMP	20.58±1.65	34.06±4.29
cis-Aconitate	0.29±0.03	0.32±0.06
Citrate	51.46±5.45	52.73±8.29
CMP	2.25±0.68	3.45±0.71
Deoxyadenosine	0.12±0.03	0.11±0.05
D-Fructose 6-phosphate	1566.58±127.26	742.25±48.54
dGMP	24.14±1.75	40.83±5.67
D-Ribose	595.12±76.88	479.47±57.68
Ectoine	3.86±0.30	5.12±0.35
Glutathione	66.38±26.11	157.70±73.26
Glycine	3348.29±90.42	3359.45±140.04
Hypoxanthine	294.79±30.12	292.80±10.21
L-Alanine	19850.41±80.37	20028.65±2937.54
L-Arginine	744.38±29.92	593.17±24.97
L-Asparagine	2761.85±92.03	2342.76±74.15
L-Aspartate	378.04±35.97	226.70±19.40
L-Citrulline	9.44±2.71	37.06±17.59a
L-Glutamate	2650.28±125.17	1243.14±287.69
L-Glutamine	2157.50±165.13	2359.28±132.24
L-Histidine	234.92±7.73	215.33±4.58
L-Lysine	331.28±38.78	254.28±38.42
L-Methionine	113.60±3.81	121.26±2.37
L-Ornithine	389.78±24.29	361.18±7.78
L-Phenylalanine	125.64±11.44	121.90±9.51
L-Proline	3670.83±265.24	4289.99±447.11
L-Serine	2934.51±57.04	2585.82±76.33
L-Threonine, L-Homoserine	6129.86±260.16	4538.40±124.77
L-Tryptophan	76.82±16.91a	44.04±8.87
L-Tyrosine	317.22±20.69	328.04±14.67
L-Valine	1379.57±63.22	2161.94±578.79
Methylmalonate	455.11±22.21	508.87±26.07
N6-Acetyl-L-Lysine	10.57±0.84	8.50±1.55
N-Acetylornithine	0.24±0.14a	0.75±0.37a
NADH	23.53±1.01	28.41±1.69
Nicotinamide	24.53±2.75	21.49±1.37
Nicotinate	0.2±0.04	0.14±0.01
Orotateb	0.17±0.12a	0.96±0.48a
Pantothenate	6.37±0.50	8.11±0.45
Phenylpyruvate	88.49±3.66	144.49±10.26
Phosphoenolpyruvate	52.02±3.75	34.76±6.10
Putrescine	1094.67±22.99	1581.56±58.11
Pyruvate	7147.32±185.27	14252.77±1819.24
SAMe	36.85±2.76	47.35±4.13
Spermidine	3340.55±55.47	2630.89±221.09
Succinate	2734.65±140.01	3108.91±173.45
UDP-Glucose	875.9217±34.03	682.39±20.57
Uracil	6.43±0.21	11.80±1.23
Uridine	3.68±0.17	3.19±0.15
Xanthine	420.93±22.16	714.83±36.36

CM2: complete medium + 2×106 cells/ml
CM4: complete medium + 4×106 cells/ml

a: concentrations between bio-reps varied widely
b: below the lower limit of quantification