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| Project | Sample ID | Sample | Sample | SEEK STRAIN ID | Treatment 1 | time after treatment | Cell culture ID | Cell culture Type | Cell culture | Cell culture | Sample | Sample | Sample | ||||||||||||||||||
| name | (unique in whole BaCell, to use in all data sheets with measurements | lab_internal_number | Organism_part | concentration | lab_internal_number | Sampling date | Age_at_sampling_hours | comments | |||||||||||||||||||||||
| Strain | glucose | Culture description | Culture_start_date | Creator | |||||||||||||||||||||||||||
| value | SD | Unit | h | Date_at_sampling | Age_at_sampling_hours | Description | |||||||||||||||||||||||||
| date | hour | ||||||||||||||||||||||||||||||
| BaCell | sample 1 | sample 1 | whole cell | 45 | 7.148627101537788 | g/l | -6.68333 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 5 | ||||||||||||||||||
| BaCell | sample 2 | sample 2 | whole cell | 45 | 6.820560170028125 | g/l | -5.68333 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 6 | ||||||||||||||||||
| BaCell | sample 3 | sample 3 | whole cell | 45 | 6.499902192462649 | g/l | -4.68333 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 7 | ||||||||||||||||||
| BaCell | sample 4 | sample 4 | whole cell | 45 | 5.7358432322795485 | g/l | -3.6833299999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 8 | ||||||||||||||||||
| BaCell | sample 5 | sample 5 | whole cell | 45 | 4.666975758290997 | g/l | -2.6833299999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 9 | ||||||||||||||||||
| BaCell | sample 6 | sample 6 | whole cell | 45 | 3.0201944509078364 | g/l | -1.6833299999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 10 | ||||||||||||||||||
| BaCell | sample 7 | sample 7 | whole cell | 45 | 1.7560740946620574 | g/l | -1.1833299999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 10.5 | ||||||||||||||||||
| BaCell | sample 8 | sample 8 | whole cell | 45 | 1.2176263811134527 | g/l | -0.6833299999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 11 | ||||||||||||||||||
| BaCell | sample 9 | sample 9 | whole cell | 45 | 0 | g/l | 2.9999999995311555E-6 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 11.683333 | ||||||||||||||||||
| BaCell | sample 10 | sample 10 | whole cell | 45 | 0 | g/l | 0.5000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 12.183333 | ||||||||||||||||||
| BaCell | sample 11 | sample 11 | whole cell | 45 | 0 | g/l | 1.0000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 12.683333 | ||||||||||||||||||
| BaCell | sample 12 | sample 12 | whole cell | 45 | 0 | g/l | 1.5000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 13.183333 | ||||||||||||||||||
| BaCell | sample 13 | sample 13 | whole cell | 45 | 0 | g/l | 2.0000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 13.683333 | ||||||||||||||||||
| BaCell | sample 14 | sample 14 | whole cell | 45 | 0 | g/l | 2.5000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 14.183333 | ||||||||||||||||||
| BaCell | sample 15 | sample 15 | whole cell | 45 | 0 | g/l | 3.0000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 14.683333 | ||||||||||||||||||
| BaCell | sample 16 | sample 16 | whole cell | 45 | 0 | g/l | 3.5000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 15.183333 | ||||||||||||||||||
| BaCell | sample 17 | sample 17 | whole cell | 45 | 0 | g/l | 4.0000029999999995 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 15.683333 | ||||||||||||||||||
| BaCell | sample 18 | sample 18 | whole cell | 45 | 0 | g/l | 5.000002999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 16.683332999999998 | ||||||||||||||||||
| BaCell | sample 19 | sample 19 | whole cell | 45 | 0 | g/l | 6.000002999999998 | Batchfermentation_Exp-Starv01 | batch | 2009-02-04T0:0:0+0000 | Praveen Kumar Sappa | 2009-02-04T0:0:0+0000 | 17.683332999999998 | ||||||||||||||||||
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| Name | 20090204_Biphase_Batch fermentation | ||||||||||
| Notes | Glucose was exhausted at time point 11.68 Hrs | ||||||||||
| cx: dry biomass [g/l] | |||||||||||
| glc - glucose [g/l] | |||||||||||
| Componentnotes | in hours | at 600 nm | |||||||||
| Components | time | OD | cx [g/l] | std. dev. | glc (g/l) | Transciptome(RNA)-sample number | Intracellular Metabolites- sample number | Extra cellular Metabolite- sample number | Intracellular Proteome- sample number | Extra cellular proteome- sample number | |
| Values | 0 | 0.13524999999999998 | 0.050625 | 0.02209708691207961 | 7.313327484738115 | ||||||
| 0.5 | 0.15575 | ||||||||||
| 1 | 0.184 | 0.05 | 0.0017677669529663656 | 7.373757032013908 | |||||||
| 1.5 | 0.22925 | ||||||||||
| 2 | 0.24774999999999997 | 0.076875 | 0.027400387770978717 | 7.273686594449334 | |||||||
| 2.5 | 0.284 | ||||||||||
| 3 | 0.345 | 0.109375 | 0.011490485194281388 | 7.2996478001277785 | |||||||
| 4 | 0.495 | 7.242866606357946 | |||||||||
| 4.5 | 0.595 | ||||||||||
| 5 | 0.72875 | 0.175 | 0.014142135623730944 | 7.148627101537788 | Sample 1 | Sample 1 | Sample 1 | 1 | |||
| 5.5 | 0.86125 | ||||||||||
| 6 | 1.056 | 0.243125 | 0.0167937860531805 | 6.820560170028125 | Sample 2 | Sample 2 | Sample 2 | 2 | |||
| 6.5 | 1.3275 | ||||||||||
| 7 | 1.735 | 0.4071 | 0.021637467504308366 | 6.499902192462649 | Sample 3 | Sample 3 | Sample 3 | 3 | |||
| 7.5 | 2.0425 | ||||||||||
| 8 | 2.7625 | 0.6725 | 0.04596194077712555 | 5.7358432322795485 | Sample 4 | Sample 4 | Sample 4 | 4 | 1 | ||
| 8.5 | 3.39375 | ||||||||||
| 9 | 4.4625 | 1.138 | 0.11030865786510136 | 4.666975758290997 | Sample 5 | Sample 5 | Sample 5 | 5 | |||
| 9.5 | 5.54375 | ||||||||||
| 10 | 6.525 | 1.6875 | 0.05303300858899119 | 3.0201944509078364 | Sample 6 | Sample 6 | Sample 6 | 6 | 2 | ||
| 10.5 | 7.3625 | 1.85 | 0.028284271247461926 | 1.7560740946620574 | Sample 7 | Sample 7 | Sample 7 | 7 | |||
| 11 | 8.3375 | 2.675 | 0.08838834764831845 | 1.2176263811134527 | Sample 8 | Sample 8 | Sample 8 | 8 | |||
| 11.45 | 9.0625 | ||||||||||
| 11.683333 | 9.6125 | 2.496875 | 0.030935921676911265 | 0 | Sample 9 | Sample 9 | Sample 9 | 9 | 3 | ||
| 12.183333 | 7.7375 | 1.91 | 0.014142135623730963 | Sample 10 | Sample 10 | Sample 10 | 10 | ||||
| 12.683333 | 6.275 | 1.735 | 0.049497474683058366 | Sample 11 | Sample 11 | Sample 11 | 11 | 4 | |||
| 13.183333 | 5.05 | 1.34 | 0.04242640687119289 | Sample 12 | Sample 12 (only LC-MS) | Sample 12 | 12 | ||||
| 13.683333 | 3.9625 | 1.105 | 0.049497474683058214 | Sample 13 | Sample 13 | 13 | 5 | ||||
| 14.183333 | 3.235 | 1.1625 | 0.03535533905932741 | Sample 14 | Sample 14 | 14 | |||||
| 14.683333 | 2.945 | 0.925 | 0.007071067811865481 | Sample 15 | Sample 15 | 15 | 6 | ||||
| 15.183333 | 2.76 | 0.825 | 0.03535533905932733 | Sample 16 | Sample 16 | 16 | |||||
| 15.683333 | 2.89 | 0.855 | 0.007071067811865481 | Sample 17 | Sample 17 | 17 | 7 | ||||
| 15.88333 | 2.835 | ||||||||||
| 16.683332999999998 | 2.93 | 0.835 | 0.007071067811865481 | Sample 18 | Sample 18 | 18 | 8 | ||||
| 17.683332999999998 | 3.285 | 0.895 | 0.007071067811865481 | Sample 19 | Sample 19 | 19 | 9 | ||||
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| Fermentation from | 2009-02-04T0:0:0+0000 | |||||||||||
| Bacillus subtilis BSG112(168 Trp+ spoIVCB::erm) | ||||||||||||
| Medium: modified after Hardiman et al. (2007), J. Biotechnology 132, 359–374. | ||||||||||||
| without Thiamin-HCl, with to 7% reduced Calcium concentration and addition of sodium molybdate (the latter analogous to the M9-Medium) | ||||||||||||
| cx: dry biomass [g/l] | ||||||||||||
| timeline: samples were usually taken in this order (sampling OD defined as t=0): | ||||||||||||
| metabolome 1 | 4 minutes before OD sampling | |||||||||||
| metabolome 2 | 2 minutes before… | |||||||||||
| OD | 0 | |||||||||||
| RNA | 1 minute after OD sampling | |||||||||||
| Proteome | 1 minute after… | |||||||||||
| extracell. Proteome | 1 minute after… | |||||||||||
| OD600nm | sampling | |||||||||||
| remarks | sample number on the tubes | time | process time [h] | process time t* [h] | OD600nm | Metabolome, Proteome, RNA | extracellular Proteome | Transcriptome | ||||
| 10:08 h inoculated | ||||||||||||
| 1 | 1899-12-31T10:8:0+0000 | 0 | -11.68333 | 0.13524999999999998 | ||||||||
| 1b | 1899-12-31T10:38:0+0000 | 0.5 | -11.18333 | 0.15575 | ||||||||
| 2 | 1899-12-31T11:8:0+0000 | 1 | -10.68333 | 0.184 | ||||||||
| 2b | 1899-12-31T11:38:0+0000 | 1.5 | -10.18333 | 0.22925 | ||||||||
| 3 | 1899-12-31T12:8:0+0000 | 2 | -9.68333 | 0.24774999999999997 | ||||||||
| 3b | 1899-12-31T12:38:0+0000 | 2.5 | -9.18333 | 0.284 | ||||||||
| 4 | 1899-12-31T13:8:0+0000 | 3 | -8.68333 | 0.345 | sampling testrun | |||||||
| 5 | 1899-12-31T14:8:0+0000 | 4 | -7.68333 | 0.495 | ||||||||
| 5b | 1899-12-31T14:38:0+0000 | 4.5 | -7.18333 | 0.595 | ||||||||
| 6 | 1899-12-31T15:8:0+0000 | 5 | -6.68333 | 0.72875 | Sample 1 | Sample 1 | ||||||
| 6b | 1899-12-31T15:38:0+0000 | 5.5 | -6.18333 | 0.86125 | ||||||||
| 7 | 1899-12-31T16:8:0+0000 | 6 | -5.68333 | 1.056 | Sample 2 | Sample 2 | ||||||
| 7b | 1899-12-31T16:38:0+0000 | 6.5 | -5.18333 | 1.3275 | ||||||||
| 8 | 1899-12-31T17:8:0+0000 | 7 | -4.68333 | 1.735 | Sample 3 | Sample 3 | ||||||
| 8b | 1899-12-31T17:38:0+0000 | 7.5 | -4.18333 | 2.0425 | ||||||||
| 9 | 1899-12-31T18:8:0+0000 | 8 | -3.6833299999999998 | 2.7625 | Sample 4 | 2 | Sample 4 | |||||
| 9b | 1899-12-31T18:38:0+0000 | 8.5 | -3.1833299999999998 | 3.39375 | ||||||||
| 10 | 1899-12-31T19:8:0+0000 | 9 | -2.6833299999999998 | 4.4625 | Sample 5 | Sample 5 | ||||||
| 10b | 1899-12-31T19:38:0+0000 | 9.5 | -2.1833299999999998 | 5.54375 | ||||||||
| 11 | 1899-12-31T20:8:0+0000 | 10 | -1.6833299999999998 | 6.525 | Sample 6 | 2 | Sample 6 | |||||
| 12 | 1899-12-31T20:38:0+0000 | 10.5 | -1.1833299999999998 | 7.3625 | Sample 7 | Sample 7 | ||||||
| 13 | 1899-12-31T21:8:0+0000 | 11 | -0.6833299999999998 | 8.3375 | Sample 8 | Sample 8 | ||||||
| 13b | 1899-12-31T21:35:0+0000 | 11.45 | -0.23333000000000048 | 9.0625 | ||||||||
| glucose exhausted; oxygen signal rises | 14 | 1899-12-31T21:49:0+0000 | 11.683333 | 2.9999999995311555E-6 | 9.6125 | Sample 9 | 2 | Sample 9 | ||||
| 15 | 1899-12-31T22:19:0+0000 | 12.183333 | 0.5000029999999995 | 7.7375 | Sample 10 | Sample 10 | ||||||
| 16 | 1899-12-31T22:49:0+0000 | 12.683333 | 1.0000029999999995 | 6.275 | Sample 11 | 2 | Sample 11 | |||||
| 17 | 1899-12-31T23:19:0+0000 | 13.183333 | 1.5000029999999995 | 5.05 | Sample 12 | Sample 12 | ||||||
| 18 | 1899-12-31T23:49:0+0000 | 13.683333 | 2.0000029999999995 | 3.9625 | 2 | Sample 13 | ||||||
| 19 | 1899-12-31T0:19:0+0000 | 14.183333 | 2.5000029999999995 | 3.235 | Sample 14 | |||||||
| 20 | 1899-12-31T0:49:0+0000 | 14.683333 | 3.0000029999999995 | 2.945 | 2 | Sample 15 | ||||||
| 21 | 1899-12-31T1:19:0+0000 | 15.183333 | 3.5000029999999995 | 2.76 | Sample 16 | |||||||
| 22 | 1899-12-31T1:49:0+0000 | 15.683333 | 4.0000029999999995 | 2.89 | 2 | Sample 17 | ||||||
| 22b | 1899-12-31T2:1:0+0000 | 15.88333 | 4.2 | 2.835 | ||||||||
| 23 | 1899-12-31T2:49:0+0000 | 16.683332999999998 | 5.000002999999998 | 2.93 | 2 | Sample 18 | ||||||
| 24 | 1899-12-31T3:49:0+0000 | 17.683332999999998 | 6.000002999999998 | 3.285 | 2 | Sample 19 | ||||||
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| Fermentation from | 2009-02-04T0:0:0+0000 | timeline: samples were usually taken in this order (sampling OD defined as t=0): | ||||||||||||||||||||||
| Bacillus subtilis BSG112 | metabolome 1 | 4 minutes before OD sampling | ||||||||||||||||||||||
| Medium: modified after Hardiman et al. (2007), J. Biotechnology 132, 359–374. | metabolome 2 | 2 minutes before… | ||||||||||||||||||||||
| without Thiamin-HCl, with to 7% reduced Calcium concentration and addition of sodium molybdate (the latter analogous to the M9-Medium) | OD | 0 | ||||||||||||||||||||||
| RNA | 1 minute after OD sampling | |||||||||||||||||||||||
| cx: dry biomass [g/l] | Proteome | 1 minute after… | ||||||||||||||||||||||
| extracell. Proteome | 1 minute after… | |||||||||||||||||||||||
| OD600nm | cx [g/l] | |||||||||||||||||||||||
| remarks | sample number | time | process time [h] | process time t* [h] | OD600nm | time | process time t* [h] | cx [g/l] | std. dev. | |||||||||||||||
| 10:08 h inoculated | ||||||||||||||||||||||||
| 1 | 1899-12-31T10:8:0+0000 | 0 | -11.68333 | 0.13524999999999998 | 10:08:00 | -11.68333 | 0.050625 | 0.02209708691207961 | ||||||||||||||||
| 2 | 1899-12-31T11:8:0+0000 | 1 | -10.68333 | 0.184 | 11:08:00 | -10.68333 | 0.05 | 0.0017677669529663656 | ||||||||||||||||
| 3 | 1899-12-31T12:8:0+0000 | 2 | -9.68333 | 0.24774999999999997 | 12:08:00 | -9.68333 | 0.076875 | 0.027400387770978717 | ||||||||||||||||
| 4 | 1899-12-31T13:8:0+0000 | 3 | -8.68333 | 0.345 | 13:08:00 | -8.68333 | 0.109375 | 0.011490485194281388 | ||||||||||||||||
| 6 | 1899-12-31T15:8:0+0000 | 5 | -6.68333 | 0.72875 | 15:08:00 | -6.68333 | 0.175 | 0.014142135623730944 | ||||||||||||||||
| 7 | 1899-12-31T16:8:0+0000 | 6 | -5.68333 | 1.056 | 16:08:00 | -5.68333 | 0.243125 | 0.0167937860531805 | ||||||||||||||||
| 8 | 1899-12-31T17:8:0+0000 | 7 | -4.68333 | 1.735 | 17:08:00 | -4.68333 | 0.4071 | 0.021637467504308366 | ||||||||||||||||
| 9 | 1899-12-31T18:8:0+0000 | 8 | -3.6833299999999998 | 2.7625 | 18:08:00 | -3.6833299999999998 | 0.6725 | 0.04596194077712555 | ||||||||||||||||
| 10 | 1899-12-31T19:8:0+0000 | 9 | -2.6833299999999998 | 4.4625 | 19:08:00 | -2.6833299999999998 | 1.138 | 0.11030865786510136 | ||||||||||||||||
| 11 | 1899-12-31T20:8:0+0000 | 10 | -1.6833299999999998 | 6.525 | 20:08:00 | -1.6833299999999998 | 1.6875 | 0.05303300858899119 | ||||||||||||||||
| 12 | 1899-12-31T20:38:0+0000 | 10.5 | -1.1833299999999998 | 7.3625 | 20:38:00 | -1.1833299999999998 | 1.85 | 0.028284271247461926 | ||||||||||||||||
| 13 | 1899-12-31T21:8:0+0000 | 11 | -0.6833299999999998 | 8.3375 | 21:08:00 | -0.6833299999999998 | 2.675 | 0.08838834764831845 | ||||||||||||||||
| glucose exhausted; oxygen signal rises | 14 | 1899-12-31T21:49:0+0000 | 11.683333 | 2.9999999995311555E-6 | 9.6125 | 21:50:00 | 0.016666 | 2.496875 | 0.030935921676911265 | |||||||||||||||
| 15 | 1899-12-31T22:19:0+0000 | 12.183333 | 0.5000029999999995 | 7.7375 | 22:19:00 | 0.5000029999999995 | 1.91 | 0.014142135623730963 | ||||||||||||||||
| 16 | 1899-12-31T22:49:0+0000 | 12.683333 | 1.0000029999999995 | 6.275 | 22:49:00 | 1.0000029999999995 | 1.735 | 0.049497474683058366 | ||||||||||||||||
| 17 | 1899-12-31T23:19:0+0000 | 13.183333 | 1.5000029999999995 | 5.05 | 23:19:00 | 1.5000029999999995 | 1.34 | 0.04242640687119289 | ||||||||||||||||
| 18 | 1899-12-31T23:49:0+0000 | 13.683333 | 2.0000029999999995 | 3.9625 | 23:49:00 | 2.0000029999999995 | 1.105 | 0.049497474683058214 | ||||||||||||||||
| 19 | 1899-12-31T0:19:0+0000 | 14.183333 | 2.5000029999999995 | 3.235 | 00:19:00 | 2.5000029999999995 | 1.1625 | 0.03535533905932741 | ||||||||||||||||
| 20 | 1899-12-31T0:49:0+0000 | 14.683333 | 3.0000029999999995 | 2.945 | 00:49:00 | 3.0000029999999995 | 0.925 | 0.007071067811865481 | ||||||||||||||||
| 21 | 1899-12-31T1:19:0+0000 | 15.183333 | 3.5000029999999995 | 2.76 | 01:19:00 | 3.5000029999999995 | 0.825 | 0.03535533905932733 | ||||||||||||||||
| 22 | 1899-12-31T1:49:0+0000 | 15.683333 | 4.0000029999999995 | 2.89 | 01:49:00 | 4.0000029999999995 | 0.855 | 0.007071067811865481 | ||||||||||||||||
| 23 | 1899-12-31T2:49:0+0000 | 16.683332999999998 | 5.000002999999998 | 2.93 | 02:49:00 | 5.000002999999998 | 0.835 | 0.007071067811865481 | ||||||||||||||||
| 24 | 1899-12-31T3:49:0+0000 | 17.683332999999998 | 6.000002999999998 | 3.285 | 03:49:00 | 6.000002999999998 | 0.895 | 0.007071067811865481 | ||||||||||||||||
