Selected Cell
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experiment
SAMPLES
chemostat_example
results RT-PCR
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| Explanations | Field | Format | Value | Remarks | |||||
| Investigation | |||||||||
| Description | text | Steady state studies for different oxygen availability in Escherichia coli | |||||||
| ID | integer | to create by SEEK | |||||||
| Comments | text | ||||||||
| Study | |||||||||
| Description | text | Determination of the impact of specific enzyme reactions and regulatory proteins using isogenic E. coli mutant strains | |||||||
| ID | integer | 3.1.3 | |||||||
| Type | text | chemostat | |||||||
| SOP | integer | ||||||||
| Comments | text | ||||||||
| Experiment | |||||||||
| Description | text | chemostat-experiments at different aerobiosis levels (mixture of argon/air) | |||||||
| ID | integer | 3.1.3.a | |||||||
| Type | text | ||||||||
| SOP | integer | SUMO Evans medium | SUMO chemostat conditions | ||||||
| Comments | |||||||||
| Culture_starting_date | date+time | 24.06.08; 12.08.08; 17.03.09; 09.07.09 | |||||||
| Assay | |||||||||
| Description | text | mRNA expression rates | by-product formation rates | DCW-estimation | intracellular metabolites | ||||
| ID | integer | ||||||||
| Type | text | transcriptomics | |||||||
| SOP | integer | SUMO mRNA isolation Epicentre | |||||||
| Experimentalist | text | Sonja Steinsiek/Christine Richter | Sonja Steinsiek | Sonja Steinsiek | Stefan Stagge | ||||
| Assay_date | date+time | ||||||||
| Culture_age | time | ||||||||
| Sampling | |||||||||
| Type | text | ||||||||
| SOP_sampling | integer | ||||||||
| SOP_sample_preparation | integer | SUMO mRNA isolation Epicentre | |||||||
| User | integer | Sonja Steinsiek | |||||||
| Group | integer | Magdeburg | |||||||
| ORGANISM | |||||||||
| Organism | integer | Escherichia coli K12 | |||||||
| NCBI_ID | integer | ||||||||
| Strain | text | MG1655 | |||||||
| Genotype | text | ||||||||
| Phenotype | text | ||||||||
| Experimental_conditions | |||||||||
| Item | text | glucose | dilution rate | 3 | 4 | 5 | 6 | ||
| SOP | |||||||||
| Start_value | float/text | 20 | 0.2 | ||||||
| End_value | float/text | ||||||||
| Unit | text | mM | 1/h | ||||||
| Comments | text | ||||||||
| FACTORS_STUDIED | |||||||||
| Factor | text | aeration | |||||||
| Start_value | float/text | 0 | |||||||
| End_value | float/text | 100 | |||||||
| Unit | text | % | |||||||
| action_time_point | |||||||||
| Comments | |||||||||
| DATA_CREATED | |||||||||
| Data_type | text | ||||||||
| Status | text | ||||||||
| Creation_date | date | 12.12.08; 09.01.09; 13.02.09; 05.05.09; 14.07.09;13.04.10;09.07.08; 10.06.08; 21.10.08; 11.11.08; 03.03.09; 10.08.09; 04.05.10; 01.02.10; 12.01.09; 10.06.08; 18.06.08; 16.06.08; 17.03.09; 24.06.08; 18.06.08; 03.02.09; 03.03.09;12.08.08; 12.10.09; 24.06.08; 12.08.08; 17.03.09; 09.07.09; 08.02.10; 08.02.10; 19.11.09;31.08.09; 10.03.2009, 18.12.09; 18.12.09 | |||||||
| Person_created | text | Sonja Steinsiek/Christine Richter | |||||||
| DATA_FILE | |||||||||
| File_name | text | ||||||||
| File_type | text | Excel sheets | |||||||
| Storage_location | text | local | |||||||
| Storage_date | date | ||||||||
| Last_change_date | date | ||||||||
| TemplateID | text | version 1 | |||||||
| PUBLICATION | |||||||||
| Title | text | ||||||||
| Authors | text | ||||||||
| Year | date | ||||||||
| Journal | text | ||||||||
| Volume | integer | ||||||||
| Issue | integer | ||||||||
| Pages | float | ||||||||
| PubmedID | text | ||||||||
| URL | text | ||||||||
| DOI | float |
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| Sample ID | chemostat_type | chemostat_ID | Experimentator ID | date | aerobiosis | Code | STRAIN | Genotype | SEEK Strain ID | |||
| sample_1 | Multi | 1 | SO | 081212 | _ | % | 0 | Multi1_SO081212_0% | 2008-12-12T0:0:0+0000 | MG1655 | wt | 61 |
| sample_2 | Multi | 1 | SO | 090119 | _ | % | 0 | Multi1_SO090119_0% | 2009-01-19T0:0:0+0000 | MG1655 | wt | 61 |
| sample_3 | Multi | 1 | SO | 090213 | _ | % | 0 | Multi1_SO090213_0% | 2009-02-13T0:0:0+0000 | MG1655 | wt | 61 |
| sample_4 | Multi | 1 | SO | 090505 | _ | % | 0 | Multi1_SO090505_0% | 2009-05-05T0:0:0+0000 | MG1655 | wt | 61 |
| sample_5 | Multi | 1 | SO | 090714 | _ | % | 0 | Multi1_SO090714_0% | 2009-07-14T0:0:0+0000 | MG1655 | wt | 61 |
| sample_6 | Multi | 1 | SO | 100413 | _ | % | 7.62 | Multi1_SO100413_7,62% | 2010-04-13T0:0:0+0000 | MG1655 | wt | 61 |
| sample_7 | Multi | 2 | SO | 080610 | _ | % | 20.18 | Multi2_SO080610_20,18% | 2008-06-10T0:0:0+0000 | MG1655 | wt | 61 |
| sample_8 | Multi | 4 | SO | 081021 | _ | % | 19.96 | Multi4_SO081021_19,96% | 2008-10-21T0:0:0+0000 | MG1655 | wt | 61 |
| sample_9 | Multi | 3 | SO | 081111 | _ | % | 19.96 | Multi3_SO081111_19,96% | 2008-11-11T0:0:0+0000 | MG1655 | wt | 61 |
| sample_10 | Multi | 2 | SO | 080709 | _ | % | 19.33 | Multi2_SO080709_19,33% | 2008-07-09T0:0:0+0000 | MG1655 | wt | 61 |
| sample_11 | Multi | 3 | SO | 090303 | _ | % | 20 | Multi3_SO090303_20% | 2009-03-03T0:0:0+0000 | MG1655 | wt | 61 |
| sample_12 | Multi | 2 | SO | 090810 | _ | % | 18.16 | Multi2_SO090810_18,16% | 2009-08-10T0:0:0+0000 | MG1655 | wt | 61 |
| sample_13 | Multi | 2 | SO | 100504 | _ | % | 38.79 | Multi2_SO100504_38,79% | 2010-05-04T0:0:0+0000 | MG1655 | wt | 61 |
| sample_14 | Multi | 2 | SO | 100201 | _ | % | 39.24 | Multi2_SO100201_39,24% | 2010-02-01T0:0:0+0000 | MG1655 | wt | 61 |
| sample_15 | Multi | 2 | SO | 090112 | _ | % | 50 | Multi2_SO090112_50% | 2009-01-12T0:0:0+0000 | MG1655 | wt | 61 |
| sample_16 | Multi | 2 | SO | 080618 | _ | % | 48.43 | Multi2_SO080618_48,43% | 18.06. | MG1655 | wt | 61 |
| sample_17 | Multi | 2 | SO | 080616 | _ | % | 53.25 | Multi2_SO080616_53,25% | 2008-06-16T0:0:0+0000 | MG1655 | wt | 61 |
| sample_18 | Multi | 1 | SO | 090317 | _ | % | 53.14 | Multi1_SO090317_53,14% | 2009-03-17T0:0:0+0000 | MG1655 | wt | 61 |
| sample_19 | Multi | 1 | SO | 080618 | _ | % | 79.6 | Multi1_SO080618_79,6% | 2008-06-18T0:0:0+0000 | MG1655 | wt | 61 |
| sample_20 | Multi | 1 | SO | 090203 | _ | % | 80.94 | Multi1_SO090203_80,94% | 2009-02-03T0:0:0+0000 | MG1655 | wt | 61 |
| sample_21 | Multi | 1 | SO | 080812 | _ | % | 78.48 | Multi1_SO080812_78,48% | 2008-08-12T0:0:0+0000 | MG1655 | wt | 61 |
| sample_22 | Multi | 1 | SO | 080624 | _ | % | 78.81 | Multi1_SO080624_78,81% | 2008-06-24T0:0:0+0000 | MG1655 | wt | 61 |
| sample_23 | Multi | 3 | SO | 090303 | _ | % | 84.08 | Multi3_SO090303_84,08% | 2009-03-03T0:0:0+0000 | MG1655 | wt | 61 |
| sample_24 | Multi | 2 | SO | 091012 | _ | % | 79.6 | Multi2_SO091012_79,6% | 2009-10-12T0:0:0+0000 | MG1655 | wt | 61 |
| sample_25 | Multi | 1 | SO | 100208 | _ | % | 95.29 | Multi1_SO100208_95,29% | 2008-08-12T0:0:0+0000 | MG1655 | wt | 61 |
| sample_26 | Multi | 2 | SO | 100208 | _ | % | 100.9 | Multi2_SO100208_100,9% | 2008-06-24T0:0:0+0000 | MG1655 | wt | 61 |
| sample_27 | Multi | 1 | SO | 080812 | _ | % | 98.65 | Multi1_SO080812_98,65% | 2009-01-19T0:0:0+0000 | MG1655 | wt | 61 |
| sample_28 | Multi | 3 | SO | 080624 | _ | % | 99.66 | Multi3_SO080624_99,66% | 2009-03-17T0:0:0+0000 | MG1655 | wt | 61 |
| sample_29 | Multi | 1 | SO | 090119 | _ | % | 100.22 | Multi1_SO090119_100,22% | 2009-08-31T0:0:0+0000 | MG1655 | wt | 61 |
| sample_30 | Multi | 3 | SO | 090317 | _ | % | 102.69 | Multi3_SO090317_102,69% | 2010-02-08T0:0:0+0000 | MG1655 | wt | 61 |
| sample_31 | Multi | 2 | SO | 090831 | _ | % | 101.46 | Multi2_SO090831_101,46% | 2010-02-08T0:0:0+0000 | MG1655 | wt | 61 |
| sample_32 | Multi | 3 | SO | 090310 | _ | % | 120.85 | Multi3_SO090310_120,85% | 2009-03-10T0:0:0+0000 | MG1655 | wt | 61 |
| sample_33 | Multi | 3 | SO | 091218 | _ | % | 118.83 | Multi3_SO091218_118,83% | 2009-12-18T0:0:0+0000 | MG1655 | wt | 61 |
| sample_34 | Multi | 4 | SO | 091218 | _ | % | 121.52 | Multi4_SO091218_121,52% | 2009-12-18T0:0:0+0000 | MG1655 | wt | 61 |
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| Parameters of bioreactor | |||||||||
| Parameter | Value | Units | Comments | ||||||
| pO2 | % | oxygenation | |||||||
| V_reactor | 1 | L | overall reactor volume | ||||||
| V_tot | 0.36 | L | total reaction volume (or working volume of broth that includes both extra- and intracellular volumes) | ||||||
| D | 0.2 | h-1 | dilution rate | ||||||
| r_gas | 0.18 | L/min | gas inflow | ||||||
| r_feed | 1.2 | mL/min | rate of feeding | ||||||
| C_glc_feed | 20 | mmol/L | glucose concentration in feed | ||||||
| T | 37 | °C | operation temperature | ||||||
| pH | 6.9 | operation pH | |||||||
| stirring | 550 | rpm | stirring rate | ||||||
| r_gas | 0.18 | L/min | gas flow rate | ||||||
| C_x | g_DW/L | dry biomass concentration | |||||||
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| Gene | gltA | sucA | sucB | sdhD | mdh | aceA | ackA | ldhA | frdA | cyoA | cydA | appC | ndh | nuoN | atpA | recA | |||||||||||||||||||||||||
| Values | |||||||||||||||||||||||||||||||||||||||||
| Unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | relative unit | |||||||||||||||||||||||||
| 0% aerobiosis | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||||||||||||||||||||
| 20% aerobiosis | 3.5747304139989318 | 1.6981808895889088 | 1.5833469273041352 | 9.658103472540864 | 2.8567890457619547 | 2.039032112059889 | 0.7577431457740929 | 0.8446844810635583 | 1.0666387266878776 | 1.7895650669483423 | 4.083422773085555 | 0.7520796604617614 | 0.77951967216992 | 1.6094262660537335 | 1.5290721741642685 | 1 | |||||||||||||||||||||||||
| 50% aerobiosis | 6.35936206502935 | 10.249908391275188 | 5.2251827136991755 | 41.246168937275826 | 7.61396365237193 | 6.638105353878887 | 0.8293174275222631 | 1.1167000355288188 | 1.8355642470706846 | 5.420401473455138 | 10.436347002009079 | 0.2487667246150085 | 0.8138832114660446 | 4.513963079459336 | 2.8728616766663664 | 1 | |||||||||||||||||||||||||
| 80% aerobiosis | 6.648449910517923 | 15.333151154856987 | 8.381389555565127 | 94.82507380003833 | 11.437862055864821 | 12.529579101303677 | 0.6816348348770269 | 1.0067018659721996 | 1.491692477055368 | 12.609943624515056 | 13.557205075896471 | 0.2218152233344897 | 0.4287398973605498 | 5.770795996360396 | 2.63971216830824 | 1 | |||||||||||||||||||||||||
| 100% aerobiosis | 9.705486118161502 | 24.868686267179797 | 17.113976465437933 | 162.9433510206598 | 18.577539159400633 | 19.013657941407804 | 0.7949901971381746 | 1.256523464937869 | 1.6470814503394198 | 31.20832993001579 | 10.890855437470641 | 0.33155676602673306 | 0.4071484055193309 | 9.455111276791877 | 3.973943691057794 | 1 | |||||||||||||||||||||||||
| 120% aerobiosis | 12.245588277503604 | 9.313572483567972 | 193.0596133941447 | 13.193860690428997 | 17.328540230565466 | 0.7909701747540098 | 0.9208598646830705 | 0.773336992246693 | 27.190932176210676 | 6.280318930209355 | 0.18315160177173553 | 0.27026034771024077 | 4.153991705543526 | 2.1506077138716932 | 1 | ||||||||||||||||||||||||||
| STDEV | |||||||||||||||||||||||||||||||||||||||||
| 0% aerobiosis | 0.10200938720121969 | 0.09236532138486175 | 0.11972808951336393 | 0.24861366989825007 | 0.12056555159351072 | 0.09085474029795446 | 0.0943959604770261 | 0.10166329355739641 | 0.09403320836520279 | 0.1168863269869617 | 0.09812076707484436 | 0.09992534896046809 | 0.1426797697955247 | 0.1490328316671547 | 0.11501114664032434 | 0.12380955603196016 | |||||||||||||||||||||||||
| 20% aerobiosis | 0.27046386985275483 | 0.1515425737910997 | 0.13528400035931812 | 1.5746818527609237 | 0.23254378777147555 | 0.22089377486166373 | 0.06869135263571807 | 0.08791360575498257 | 0.07972613525731494 | 0.14085072868895826 | 0.3914449455811643 | 0.16387162132797978 | 0.05489138378979164 | 0.1372038864963358 | 0.10822119329210672 | 0.08468959771583048 | |||||||||||||||||||||||||
| 50% aerobiosis | 0.867921195665072 | 1.346910760369321 | 1.007781146968274 | 5.012722956489456 | 0.8932218361124776 | 0.9560930720507896 | 0.11214714787372547 | 0.1368494394253412 | 0.23011967161488453 | 1.10277931714082 | 1.2406314017553193 | 0.02982851037208196 | 0.11564626489726389 | 0.5700140269374891 | 0.3868082185244811 | 0.16422407931886995 | |||||||||||||||||||||||||
| 80% aerobiosis | 1.0498371065907055 | 1.9503984635193112 | 1.4985614414554493 | 12.63265071989937 | 1.501749514899028 | 1.7800264005911264 | 0.10503182642907559 | 0.1384788662098157 | 0.21110815254273987 | 1.8843101777117766 | 2.0404712349559713 | 0.05149771254640294 | 0.0770571628918485 | 0.756426093602737 | 0.37268266586221355 | 0.16918566511210845 | |||||||||||||||||||||||||
| 100% aerobiosis | 1.0580374396330354 | 2.9368298942900504 | 2.3506267278166466 | 18.345300223159875 | 2.0009773814267673 | 2.038321674892573 | 0.11631721772314692 | 0.15019765809639002 | 0.18326040406027594 | 3.2312275842083165 | 1.6202142591520619 | 0.046546826173507784 | 0.06784297272720181 | 1.1493046314803521 | 0.4302689102698745 | 0.14087326183917573 | |||||||||||||||||||||||||
| 120% aerobiosis | 0 | 0.4416249809012255 | 13.517096181542852 | 0.45699907442762705 | 0.3006951782279148 | 0.07999298760635308 | 0.06125254755032508 | 0.0314929600207949 | 0.511865188539268 | 0.32862716686321836 | 0.010943618639487184 | 0.015109493575378167 | 0.16431165293066716 | 0.12613487797410466 | 0 | ||||||||||||||||||||||||||
