Selected Cell
Cell:
Value:
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 | M49 | ||||||||
| Strain | Streptococcus pyogenes | ||||||||
| Vessel type | 50 ml Greiner tube | ||||||||
| Temperature (degree celcius) | 37 | ||||||||
| Volume (ml) | 20 | ||||||||
| Gas flow (ml/min) | ±10 | ||||||||
| pH | 6.5 | ||||||||
| Explanations | Data | ||||||||
| Seek assay ID | 22 | ||||||||
| 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 | S. pyogenes | ||||||||
| Strain | M49 | ||||||||
| 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 | 5 | ||||||||
| Unit | mM | ||||||||
| Comments | Cultures were pulsed with 5 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 | 2010-08-01T0:0:0+0000 | ||||||||
| Last_change_date | 19/04/2010 | ||||||||
| TemplateID | Glucose pulse template | ||||||||
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| Decription experiment | |||||||||
| M49 (s. pyogenes) was grown Overnight in THY medium | |||||||||
| The culture was diluted to OD=0.05 in THY 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 10 ml indicated medium/buffer | |||||||||
| OD here is around 20 | |||||||||
| Suspension was incubated under anaerobic flushing at 37 degree celcius for 10 minutes | |||||||||
| Approximately 5 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 | 1 | 10 | 50 | ||||
| OD1 | 600 nm | 18 | 29 | 23.2 | 18.4 | ||||
| OD2 | 600 nm | 23.5 | 29.7 | 26.7 | 21.7 | ||||
| Average OD 1 + 2 | 600 nm | 20.75 | 29.35 | 24.95 | 20.049999999999997 | ||||
| stdev OD 1+ 2 | 600 nm | 3.8890872965260113 | 0.49497474683024334 | 2.474873734152962 | 2.3334523779156418 | ||||
| Calculated dryweights | g/l | 6.916666666666667 | 9.783333333333333 | 8.316666666666666 | 6.683333333333333 | ||||
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| Experiment ID | Identifier | Unit | |||||||||||||||||||||||||||||
| Time after glucose-pulse | min | -0.1 | -0.05 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | Maximal value | |||||||||||||||||
| Metabolite | |||||||||||||||||||||||||||||||
| 1 | FBP | mM | -0.36358127556430686 | -0.02693194633808771 | 2.545068928950159 | 2.7874564459930373 | 4.5245669848002885 | 2.9490481240216173 | 2.518136982612062 | 3.3799592654311628 | 4.309111414095508 | 4.659226716490766 | 4.066723897052631 | 4.659226716490766 | |||||||||||||||||
| 2 | FBP | mM | 0.3602834862167861 | -0.02844343312237796 | 0.9291521486643468 | 0.9196710042902181 | 1.3842470786224021 | 1.3463225011258855 | 1.972078029818202 | 1.7729739979615529 | 1.422171656118893 | 2.379767237905623 | 1.9815591741923246 | 1.8962288748251914 | 2.379767237905623 | ||||||||||||||||
| 3 | FBP | mM | -0.07820519086953759 | 0.21227123236020096 | 3.4633727385083795 | 4.692311452172642 | 5.641945912731386 | 6.770335095277664 | 6.133521398197092 | 6.334620460433065 | 1.530587307018222 | 0.7708797385712227 | 0.5362641659625871 | -0.3575094439750526 | 6.770335095277664 | ||||||||||||||||
| 4 | FBP | mM | 0.8598124360774526 | 0.45764210307347675 | 3.2728344341012745 | 5.020195191290933 | 5.685856432125089 | 6.406989443028757 | 7.280669821623588 | 5.852271742333627 | 2.607173193267123 | 1.983115779985086 | 0.8459444935600744 | 0.4715100455908612 | 7.280669821623588 | ||||||||||||||||
| 1 | G6P | mM | -0.14294222751637836 | 0.09529481834425275 | 1.1911852293031564 | 1.0800079412348618 | 1.14353782013103 | 1.3023625173714513 | 0.7782410164780622 | 1.0800079412348615 | 1.2547151081993249 | 0.9688306531665675 | 0.9053007742703988 | 1.3023625173714513 | |||||||||||||||||
| 2 | G6P | mM | -0.05591277606933248 | -0.10064299692479729 | 0.2907464355605257 | 0.5926754263349175 | 0.3242941012021253 | 0.45848476376852054 | 0.49203242941012004 | 0.525580095051719 | 0.436119653340789 | 0.49203242941012026 | 0.5591277606933184 | 0.6150405367626502 | 0.6150405367626502 | ||||||||||||||||
| 3 | G6P | mM | -0.14494742910478528 | -0.07906223405715561 | 1.199110549866857 | 1.3045268619430643 | 1.6207757981716864 | 1.5680676421335829 | 1.594421720152634 | 1.7130150712383674 | -0.30307189721909533 | -0.21083262415241447 | -0.0658851950476295 | 0.03953111702857827 | 1.7130150712383674 | ||||||||||||||||
| 4 | G6P | mM | 0.16356573297894092 | 0.2944183193620932 | 0.8178286648947054 | 1.0795338376610097 | 1.586587609895727 | 1.6520139030873031 | 1.3575955837252094 | 1.3412390104273153 | 0.13085258638315267 | -0.47434062563892854 | -0.19627887957472911 | -0.13085258638315322 | 1.6520139030873031 | ||||||||||||||||
| 1 | F6P | mM | 0.21357742181540723 | 0.12204424103737563 | 0.27459954233409567 | 0.24408848207475295 | 0.488176964149505 | 0.3356216628527841 | -0.09153318077803119 | 0.3356216628527867 | 0.45766590389016015 | -0.0610221205186863 | 0.48817696414950457 | 0 | 0.488176964149505 | ||||||||||||||||
| 2 | F6P | mM | 0.06444683136412549 | -0.04296455424275032 | 0.32223415682062295 | -0.12889366272824948 | 0.25778732545649896 | 0.40816326530612335 | 0.06444683136412552 | 0.3866809881847487 | -0.945220193340495 | 0.19334049409237347 | -0.04296455424274881 | -0.10741138560687279 | 0.40816326530612335 | ||||||||||||||||
| 3 | F6P | mM | -0.050627570931335686 | 0.10125514186267236 | 0.20251028372534652 | 0.2784516401223486 | 0.025313785465666747 | 0.3037654255880168 | -0.25313785465668176 | 0.2531378546566818 | -0.227824069191015 | -0.6328446366417045 | -0.4050205674506909 | -0.2025102837253447 | 0.3037654255880168 | ||||||||||||||||
| 4 | F6P | mM | -0.06284367635506764 | -0.5027494108405344 | 0.5655930871955996 | -0.09426551453259924 | 0.1885310290652012 | 0.34564021995286764 | 0.5341712490180661 | 0.5655930871955999 | -0.6284367635506695 | 0.18853102906520075 | 0.1571091908876669 | -0.03142183817753347 | 0.5655930871955999 | ||||||||||||||||
| 1 | ATP | mM | -0.0313356835095959 | 0 | 0.7207207207207207 | 1.5824520172346253 | 2.224833529181355 | 1.6294555424990207 | 1.4257735996866423 | 1.3317665491578532 | 1.7234625930278102 | 1.6921269095182139 | 1.034077555816686 | 0 | 2.224833529181355 | ||||||||||||||||
| 2 | ATP | mM | 0.011031439602868329 | 0.11031439602868175 | 0.02206287920573665 | 0.45228902371759516 | 0.8825151682294534 | 0.9266409266409258 | 1.0038610038610039 | 1.1252068394925536 | 1.047986762272476 | 1.2906784335355763 | 1.1803640375068944 | 1.2465526751241036 | 1.2906784335355763 | ||||||||||||||||
| 3 | ATP | mM | 0.07799382548881487 | 0.14298868006282855 | 0.662947516654931 | 1.2868981205654557 | 1.6508693061799276 | 1.7028651898391385 | 2.0018415208795974 | 1.780859015327953 | 1.7938579862427555 | 1.0659156150138114 | 0.7929372258029572 | 0.5979526620809188 | 2.0018415208795974 | ||||||||||||||||
| 4 | ATP | mM | 0.112948769665188 | 0.12908430818878647 | 0.6615570794675272 | 1.4844695441710367 | 2.323517547398144 | 2.226704316256554 | 2.258975393303752 | 1.8878580072609923 | 2.371924162968939 | 0.7260992335619201 | 0.8551835417507061 | 0.7906413876563128 | 2.371924162968939 | ||||||||||||||||
| 1 | PYR | mM | -12.90821256038647 | -9.623188405797086 | -6.879227053140093 | -2.396135265700458 | -9.31400966183575 | -8.193236714975825 | -8.772946859903358 | -2.5120772946859873 | -8.154589371980677 | -4.367149758454129 | -1.7391304347825915 | -1.7391304347825915 | |||||||||||||||||
| 2 | PYR | mM | -3.755102040816327 | 1.2789115646258384 | -2.312925170068027 | -2.9387755102040813 | -2.9115646258503407 | -5.251700680272133 | 1.333333333333357 | -3.8095238095238297 | -4.3537414965986425 | -0.7891156462585016 | 4.653061224489788 | 1.6054421768707385 | 4.653061224489788 | ||||||||||||||||
| 3 | PYR | mM | 1.3466933867735609 | -2.4368737474949924 | -5.354709418837691 | -0.7374749498998021 | -0.8016032064128247 | 0.9298597194388769 | -4.072144288577173 | -4.1683366733466976 | -2.91783567134269 | -1.442885771543093 | 2.6933867735470898 | -4.0400801603206435 | 2.6933867735470898 | ||||||||||||||||
| 4 | PYR | mM | 0.9154228855721573 | 6.726368159204016 | 3.064676616915424 | -1.3532338308457952 | 5.412935323383085 | 1.2338308457711484 | 5.651741293532339 | 2.0298507462686572 | 0.35820895522387275 | 3.184079601990053 | 2.2686567164179117 | 13.452736318407965 | 13.452736318407965 | ||||||||||||||||
| 1 | PEP | mM | 7.0338164251207465 | -3.1690821256038815 | 1.1594202898550705 | 8.541062801932366 | 2.2801932367149664 | 0.15458937198067613 | -0.27053140096615724 | -6.72463768115942 | 5.913043478260853 | -2.125603864734299 | 1.0048309178743708 | 0 | 8.541062801932366 | ||||||||||||||||
| 2 | PEP | mM | -0.02721088435375263 | -1.7687074829931984 | 0.16326530612242518 | 2.448979591836766 | 1.8503401360544087 | 2.013605442176895 | 0.4625850340136184 | 1.06122448979592 | 0.24489795918366042 | 1.7959183673469137 | 0.870748299319728 | 1.4149659863945585 | 2.448979591836766 | ||||||||||||||||
| 3 | PEP | mM | 1.0581162324649158 | 3.751503006012009 | 1.3146292585170491 | 1.7635270541082164 | 1.2184368737475095 | 2.757515030060121 | 1.5070140280560906 | -0.12825651302608243 | 3.4308617234468946 | 2.3727454909819645 | 5.130260521042064 | 3.559118236472956 | 5.130260521042064 | ||||||||||||||||
| 4 | PEP | mM | 2.945273631840777 | 0.19900497512437898 | 2.587064676616915 | 0.5174129353234012 | 4.77611940298512 | 4.1393034825870645 | -0.7562189054726378 | 5.61194029850744 | 2.587064676616915 | 5.293532338308486 | 3.422885572139317 | 6.169154228855737 | 6.169154228855737 | ||||||||||||||||
| 1 | 2PGA | mM | 2.6811594202898883 | 0.676328502415448 | 0.579710144927525 | 3.4541062801931983 | -0.8212560386473102 | -1.9806763285023992 | 0.38647342995167433 | 3.067632850241546 | -0.6763285024154477 | 2.753623188405819 | -0.48309178743960524 | 0 | 3.4541062801931983 | ||||||||||||||||
| 2 | 2PGA | mM | 0.22108843537415712 | -1.1394557823129174 | 0.23809523809524968 | -0.5952380952381149 | -0.05102040816326525 | -0.714285714285722 | -2.925170068027218 | 0.03401360544217069 | -0.7993197278911486 | -0.5272108843537167 | 1.2585034013605445 | 0.30612244897959195 | 1.2585034013605445 | ||||||||||||||||
| 3 | 2PGA | mM | -0.44088176352705366 | 0.28056112224448015 | -0.5210420841683365 | 0.20040080160318774 | 1.1623246492985881 | 0.7815631262525001 | 0.3206412825651572 | 1.2625250501002094 | 1.0420841683366597 | 0.6012024048096287 | 0.3807615230461012 | 0.6613226452905745 | 1.2625250501002094 | ||||||||||||||||
| 4 | 2PGA | mM | -0.3233830845771315 | 0.7711442786069709 | 0.8208955223880201 | 4.5771144278606855 | 0.14925373134326003 | 0.199004975124367 | 0.22388059701492535 | 1.4427860696517234 | 0.6467661691542288 | 0.7462686567164176 | 1.1940298507462774 | 1.3681592039800994 | 4.5771144278606855 | ||||||||||||||||
| 1 | PYR | mM | -0.23332523176277586 | -2.3665844935939626 | -2.29992014166176 | -3.4332141245095658 | -4.2665185236623735 | -4.333182875594586 | -2.2999201416617465 | -2.1332592618311725 | -0.8666365751189051 | 4.733168987187956 | -3.6998715322384648 | 4.733168987187956 | |||||||||||||||||
| 2 | PYR | mM | -0.8719174820437026 | -0.8012214699861175 | -2.615752446131114 | -2.0030536749652716 | -2.5686217714260486 | -2.568621771426047 | -1.7202696267348765 | -1.72026962673488 | -0.6126987711658227 | -1.626008277324745 | -1.34322422909435 | -0.6126987711658227 | |||||||||||||||||
| 3 | PYR | mM | 0.1663268900914341 | -0.9425190438513829 | -0.4712595219256963 | 0.19404803843999208 | 0.582144115319986 | 0.38809607687997527 | -1.358336269079956 | -1.3028939723828046 | -0.2217691867885545 | -1.1365670822913838 | -2.245413016234199 | 0.582144115319986 | |||||||||||||||||
| 4 | PYR | mM | 1.034876784982787 | -0.13798357133102357 | 0.06899178566551889 | 1.5523151774741972 | -0.06899178566551889 | -1.2073562491465868 | 0.27596714266207734 | -1.3453398204776086 | 0.03449589283275856 | 0.827901427986216 | 4.484466068258747 | 4.484466068258747 | |||||||||||||||||
| 1 | ADP | mM | -1.592958660991295 | -1.2466632999062135 | 1.1081451554722097 | 2.56258567202946 | -1.246663299906178 | 2.1470312387273403 | 0.13851814443402333 | -2.9088810331144863 | 3.3936945386335537 | -2.8396219608974818 | -1.1081451554722364 | 3.3936945386335537 | |||||||||||||||||
| 2 | ADP | mM | 0.8324067367819943 | 1.273092656254784 | -0.19586040865459964 | 1.0282671454365548 | -1.0772322476001808 | 1.6158483714002987 | -0.7834416346183275 | -2.7910108233277917 | 1.1751624519274522 | 1.8606738822185296 | 0.4406859194727879 | 1.8606738822185296 | |||||||||||||||||
| 3 | ADP | mM | -1.3248052992211985 | 2.1888087552349944 | -0.5760023040092133 | 2.707210828843298 | 2.3040092160368637 | 0.5184020736083141 | 0.7488029952120243 | 0.40320161280645195 | 2.649610598442372 | 0.6912027648110595 | 4.2624170496681515 | 4.2624170496681515 | |||||||||||||||||
| 4 | ADP | mM | 3.0104379769140266 | 7.597772036973414 | 7.669449131661887 | 5.877521764451098 | 0.7884480415727158 | 4.372302775994122 | 3.7988860184867193 | 6.881001090089146 | 3.1537921662908595 | 5.160750817566857 | -3.0104379769140053 | 7.669449131661887 | |||||||||||||||||
| 1 | AMP | mM | 4.9692101740294525 | 2.4846050870147316 | 1.970548862115125 | -0.856760374832696 | 3.769745649263651 | 1.0281124497991865 | -0.7710843373493965 | 0.6854082998661308 | -1.3708165997322332 | 0.6854082998660935 | 3.3413654618473903 | 4.9692101740294525 | |||||||||||||||||
| 2 | AMP | mM | 3.0285822449365902 | 1.9382926367594369 | 1.9988642816581557 | 0.9085746734809756 | 3.0285822449365867 | 0.12114328979748379 | 0.42400151429112043 | 2.9074389551391473 | 1.4537194775695834 | -0.12114328979748379 | 1.0902896081771907 | 3.0285822449365902 | |||||||||||||||||
| 3 | AMP | mM | 6.127811177911374 | 5.700289467824536 | 7.054108216432866 | 0.4275217100868698 | 3.4914272990425292 | 0.35626809173903595 | 2.850144733912245 | 3.8476953907815616 | 1.5675796036517262 | 4.417724337564017 | 5.629035849476756 | 7.054108216432866 | |||||||||||||||||
| 4 | AMP | mM | 12.945414242172353 | 7.802715433638127 | 7.004710446106952 | 3.1920199501247577 | 6.738708783596563 | 5.5860349127182065 | 2.128013300083124 | -2.660016625103939 | 4.078692158492627 | 6.118038237738986 | 5.67470213355497 | 12.945414242172353 |
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| Experiment ID | Measurement technique | Identifier | Unit | |||||||||||||||||||||||||||
| Time | min | 0 | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ||||||||||||||||||
| 1 | Enzymatic | Glucose | mM | 2.472280006428158 | 2.004526470761304 | 1.9363891446995964 | 1.356761485836831 | 1.385765888146882 | 1.3903697615294295 | 1.2117394742865764 | 0.9603679875994671 | 0.007826584750331173 | ||||||||||||||||||
| 1 | Enzymatic | Lactate | mM | 0.54313725490196 | 0.37843137254901815 | 0.9117647058823529 | 3.3 | 3.6725490196078434 | 3.9470588235294133 | 5.201960784313726 | 7.4490196078431365 | 8.59019607843137 | 9.931372549019606 | 9.617647058823529 | ||||||||||||||||
| 1 | Added | Phosphate | mM | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||||||||||||||||
| 2 | Enzymatic | Glucose | mM | 1.7029468821223759 | 1.8061261943610596 | 1.411310718823131 | 1.5268585290588808 | 1.7175937876452174 | 1.5375995931089645 | 1.731589719589266 | 1.6280849205611858 | -0.015297879101634458 | ||||||||||||||||||
| 2 | Enzymatic | Lactate | mM | 0.5039215686274507 | 0.14705882352941177 | 0.8921568627450992 | 2.0372549019607837 | 2.1313725490196056 | 3.088235294117647 | 5.033333333333333 | 4.127450980392158 | 5.350980392156864 | 5.25686274509804 | 6.127450980392158 | ||||||||||||||||
| 2 | Added | Phosphate | mM | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||||||||||
| 3 | Enzymatic | Glucose | mM | 1.9917795539971193 | 1.7306504390747748 | 1.0985035640941436 | 0.7236569313830364 | 0.4234733154019251 | 0.050924006282510016 | 0.004977534448666432 | -0.006126196244512538 | -0.0042117599181023336 | ||||||||||||||||||
| 3 | Enzymatic | Lactate | mM | 0.40588235294117514 | 0.21764705882352875 | 0.9745098039215684 | 3.966666666666667 | 6.221568627450983 | 8.688235294117646 | 13.303921568627452 | 13.74313725490196 | 14.182352941176472 | 15.719607843137252 | 12.82549019607843 | ||||||||||||||||
| 3 | Added | Phosphate | mM | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | ||||||||||||||||
| 4 | Enzymatic | Glucose | mM | 2.4213733366570445 | 1.9620652106166285 | 1.452252249140234 | 0.7180262924718941 | 0.6608510070726722 | 0.14436759563303508 | -0.021917192736368437 | -0.009529214233203603 | -0.013340899926485145 | ||||||||||||||||||
| 4 | Enzymatic | Lactate | mM | 0.386274509803923 | 0.37843137254901815 | 1.0333333333333332 | 2.233333333333335 | 5.719607843137252 | 4.919607843137254 | 11.158823529411764 | 8.53529411764706 | 14.80980392156863 | 14.045098039215688 | 13.405882352941175 | ||||||||||||||||
| 4 | Added | Phosphate | mM | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | ||||||||||||||||
| Calculated rate value | rate lactate | OD | qlac | rate glucose | qgluc | |||||||||||||||||||||||||
| Unit | AU | 600 nm | mmol/g/h | mmol/g/h | ||||||||||||||||||||||||||
| 1 | 1.11 | 20.75 | 9.628915662650604 | -0.24 | -2.0819277108433734 | |||||||||||||||||||||||||
| 2 | 0.66 | 29.35 | 4.047700170357752 | -0.11 | -0.6746166950596252 | |||||||||||||||||||||||||
| 3 | 2.12 | 24.95 | 15.294589178356714 | -0.45 | -3.246492985971944 | |||||||||||||||||||||||||
| 4 | 1.89 | 20.05 | 16.967581047381543 | -0.48 | -4.309226932668329 | |||||||||||||||||||||||||
