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Metadata
Description
Data internal metabolites
Data external metabolites
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| Item | Value | ||||||||
| Experimentator | Martijn | ||||||||
| Project | SYSMO-LAB | ||||||||
| Description | Glucose pulsed cells for analysis of changes of the metabolome | ||||||||
| Aim | Change in metabolome in time upon glucose-pulse | ||||||||
| Strain information | NZ9000 | ||||||||
| Strain | Streptococcus pyogenes | ||||||||
| Vessel type | 50 ml Greiner tube | ||||||||
| Temperature (degree celcius) | 37 | ||||||||
| Volume (ml) | 20 | ||||||||
| Gas flow (ml/min) | ±400 | ||||||||
| pH | 6.5 | ||||||||
| Explanations | Data | ||||||||
| Seek assay ID | 27 | ||||||||
| EXPERIMENT | |||||||||
| Experiment_description | Glucose pulse | ||||||||
| Experiment_type | time series | ||||||||
| Experimentalist | Martijn Bekker | ||||||||
| Begin_date | 2010-08-01T0:0:0+0000 | ||||||||
| User | Martijn Bekker | ||||||||
| Group | University of Amsterdam | ||||||||
| ORGANISM | |||||||||
| Organism | L. lactis | ||||||||
| Strain | NZ9000 | ||||||||
| Genotype | wild-type | ||||||||
| Phenotype | wild-type | ||||||||
| Culture_starting_date | 2010-07-01T0:0:0+0000 | ||||||||
| Date_at_sampling | 2010-08-01T0:0:0+0000 | ||||||||
| Experimental_conditions | |||||||||
| Item | pH | temperature | buffer | ||||||
| Start_value | 6.5 | 37 | 100 mM MES buffer | ||||||
| End_value | 6.5 | 37 | 100 mM MES buffer | ||||||
| Unit | dimensionlesss | ºC | Concentration | ||||||
| Comments | |||||||||
| FACTORS_STUDIED | |||||||||
| Item | Glucose | ||||||||
| Start_value | 0 | ||||||||
| End_value | 20 | ||||||||
| Unit | mM | ||||||||
| Comments | Cultures were pulsed with 20 mM glucose | ||||||||
| DATA_CREATED | |||||||||
| Datatype | External and intracellular metabolite concentrations | ||||||||
| Creation_date | 2010-08-01T0:0:0+0000 | ||||||||
| Status | row, normalised, .... | ||||||||
| Person_created | Martijn Bekker | ||||||||
| DATA_FILE | |||||||||
| File_name | Glucose pulsed S pyogenes | ||||||||
| File_type | excel sheet | ||||||||
| Storage_location | SYSMO-Seek | ||||||||
| Storage_date | 16/07/2009 | ||||||||
| Last_change_date | 19/04/2010 | ||||||||
| TemplateID | Glucose pulse template | ||||||||
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| Decription experiment | |||||||||
| NZ9000 (L. lactis) was grown overnight in LAB medium | |||||||||
| The culture was diluted to OD=0.05 in LAB medium | |||||||||
| Growth at 37 degree celcius non-shaking in a 1 liter bottle with 1 liter medium was performed till OD=0.88 and 0.94 | |||||||||
| The culture was centrifuged 10 minutes at 6000 RPM | |||||||||
| The pellet was resuspended in indicated medium/buffer | |||||||||
| The suspension was centrifuged for 10 minutes at 6000 RPM | |||||||||
| Total pellet was resuspended in 20 ml indicated medium/buffer | |||||||||
| OD here is around 20 | |||||||||
| Suspension was incubated under anaerobic flushing at 37 degree celcius for 10 minutes | |||||||||
| Approximately 20 mM glucose-pulse (final concentration) was performed and samples for internal metabolites (SOP8) were taken in time | |||||||||
| Identifier | Unit | ||||||||
| Experiment ID | 1 | 2 | 3 | 4 | |||||
| Phosphate concentration (mM) | mM | 0 | 20 | 50 | |||||
| OD1 | 600 nm | 12.5 | 12.9 | 11.5 | |||||
| OD2 | 600 nm | ||||||||
| Average OD 1 + 2 | 600 nm | 12.5 | 12.9 | 11.5 | |||||
| stdev OD 1+ 2 | 600 nm | ||||||||
| Calculated dryweights | g/l | 4.166666666666667 | 4.3 | 3.8333333333333335 | |||||
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| Experiment ID | Identifier | Unit | |||||||||||||||||||||||||||||
| Time after glucose-pulse | min | -0.1 | 1 | 2 | 3 | 4 | 5 | 6 | 10 | 15 | 20 | 25 | 30 | Maximal value | |||||||||||||||||
| Metabolite | |||||||||||||||||||||||||||||||
| Average | |||||||||||||||||||||||||||||||
| 1 | FBP | mM | -0.6954870617327602 | 12.695398745915394 | 17.894992493155527 | 16.791044776119403 | 15.190320586417027 | 13.534399010862845 | 12.220701227589862 | 10.465424357502428 | 11.359622008301688 | 11.083635079042656 | 9.95760840766582 | 9.240042391592336 | 17.894992493155527 | ||||||||||||||||
| 2 | FBP | mM | -0.2776813606386672 | 17.675486609884388 | 26.294288842015323 | 23.37863455530932 | 32.21103783408539 | 33.214962753317494 | 32.253758043414415 | 36.97434117427175 | 32.093557258430565 | 31.87995621178543 | 27.682695645208664 | 15.389955410781516 | 36.97434117427175 | ||||||||||||||||
| 3 | FBP | mM | 0.07194395565854173 | 15.216146621781629 | 20.53999934051374 | 25.935796014904394 | 27.002964690506094 | 26.943011394123975 | 25.3842256881889 | 30.86395697751451 | 43.526093173417905 | 47.89069315003613 | 43.35822394354798 | 39.89292341266153 | 47.89069315003613 | ||||||||||||||||
| Stdev | |||||||||||||||||||||||||||||||
| 1 | FBP | mM | 0.0156121783358459 | 1.9359101136432693 | 2.0139710053224045 | 0.6400993117691421 | 1.6861152602699665 | 0.6400993117691421 | 0.7337723817840734 | 2.497948533733273 | 2.0139710053224467 | 1.654890903598298 | 1.654890903598298 | 1.5143812985758014 | |||||||||||||||||
| 2 | FBP | mM | 0.10572712398591379 | 3.202021469287875 | 5.271252324440911 | 6.101965441473106 | 9.9836612792419 | 9.017013288513462 | 9.394610159891748 | 15.859068597888033 | 0.49842787021935236 | 0.709882118191733 | 1.3291409872515112 | 0.830713117032216 | |||||||||||||||||
| 3 | FBP | mM | 0.20348823564616267 | 0.08478676485370633 | 1.4752897084345562 | 4.459783831244929 | 0.94961176634895 | 1.102227943083433 | 2.0518397094320715 | 2.1027117683437635 | 11.564914725889937 | 11.395341196184805 | 6.3759647169129385 | 4.425869125303977 | |||||||||||||||||
| Average | |||||||||||||||||||||||||||||||
| 1 | NAD | mM | 4.846153846153847 | 5.26923076923077 | 2.5 | 3 | 2.884615384615385 | 3.5961538461538463 | 1.6730769230769227 | 3.9615384615384603 | 5.4230769230769225 | 5.4230769230769225 | 3.384615384615384 | 4.673076923076922 | 5.4230769230769225 | ||||||||||||||||
| 2 | NAD | mM | 1.7116279069767446 | 2.8279069767441865 | 1.879069767441861 | 2.902325581395349 | 4.111627906976745 | 5.823255813953487 | 4.260465116279071 | 3.627906976744187 | 2.0093023255813964 | 2.5488372093023264 | 1.506976744186047 | 2.6418604651162796 | 5.823255813953487 | ||||||||||||||||
| 3 | NAD | mM | 2.7780678851174927 | 4.198433420365535 | 3.822454308093993 | 3.6762402088772834 | 1.5665796344647522 | 1.8590078328981732 | 1.8172323759791125 | 5.4725848563968675 | 1.7754569190600522 | 2.6527415143603132 | 1.3577023498694514 | 2.151436031331593 | 5.4725848563968675 | ||||||||||||||||
| Stdev | |||||||||||||||||||||||||||||||
| 1 | NAD | mM | 0.2175713172881731 | 0.3807498052542936 | 1.3054279037290122 | 0.21757131728818127 | 0 | 1.985338270254538 | 1.3870171477120732 | 2.3932844901698536 | 0.7614996105085918 | 0.43514263457633806 | 0.8158924398306295 | 3.508337491271716 | |||||||||||||||||
| 2 | NAD | mM | 0.05262189999528137 | 0.578840899948059 | 0.289420449974028 | 0.3683532999669419 | 0.4999080499551537 | 0.05262189999542484 | 2.8942044997402876 | 1.1050598999008368 | 1.7628336498418116 | 0.9998160999102808 | 0.1052437999905543 | 0.8682613499220875 | |||||||||||||||||
| 3 | NAD | mM | 1.0634295194868175 | 0.29539708874632037 | 4.312797495696541 | 2.688113507591679 | 0.17723825324780293 | 0.9748103928629176 | 1.2406677727346214 | 0.08861912662387766 | 0.17723825324780543 | 1.0634295194868175 | 0.6498735952419447 | 0.41355592424487864 | |||||||||||||||||
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| Experiment ID | Measurement technique | Identifier | Unit | |||||||||||||||||||||||||||
| Time | min | -0.1 | 6 | 11 | 21 | 31 | 61 | |||||||||||||||||||||||
| 1 | HPLC | Glucose | mM | 0 | 20.3727 | 16.787 | 9.7418 | 3.737 | 0 | |||||||||||||||||||||
| 1 | HPLC | Lactate | mM | 0 | 10.1139 | 15.9325 | 26.7781 | 36.5451 | 46.4877 | |||||||||||||||||||||
| 1 | HPLC | Phosphate | mM | 0 | 0 | 0 | 0 | 0 | 0 | |||||||||||||||||||||
| 2 | HPLC | Glucose | mM | 0 | 19.3481 | 14.2353 | 4.8243 | 0 | 0 | |||||||||||||||||||||
| 2 | HPLC | Lactate | mM | 0 | 13.8373 | 21.0408 | 36.4141 | 48.156 | 50.3032 | |||||||||||||||||||||
| 2 | HPLC | Phosphate | mM | 22.5937 | 21.4459 | 21.3693 | 21.2807 | 21.8909 | 23.2537 | |||||||||||||||||||||
| 3 | HPLC | Glucose | mM | 0 | 20.2025 | 16.0312 | 7.5502 | 0 | 0 | |||||||||||||||||||||
| 3 | HPLC | Lactate | mM | 0 | 10.8932 | 17.6905 | 30.0184 | 42.4398 | 49.1808 | |||||||||||||||||||||
| 3 | HPLC | Phosphate | mM | 47.7847 | 45.6934 | 45.7619 | 45.3886 | 48.568 | 49.8915 | |||||||||||||||||||||
| Calculated rate value | rate lactate | OD | qlac | rate glucose | qgluc | |||||||||||||||||||||||||
| Unit | AU | 600 nm | mmol/g/h | mmol/g/h | ||||||||||||||||||||||||||
| 1 | 12.5 | -0.6677 | -9.61488 | |||||||||||||||||||||||||||
| 2 | 12.9 | -0.9644 | -13.456744186046514 | |||||||||||||||||||||||||||
| 3 | 11.5 | -0.8441 | -13.212 | |||||||||||||||||||||||||||
