{"text_format":"2","workbook":"xls","n_sheets":4,"sheets":["experiment","SAMPLES","chemostat_example","results RT-PCR"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":1,"defined_names":11,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"experiment","index":0,"n_rows":89,"n_cols":9,"rows_kept":89,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Explanations","Field","Format","Value","Remarks"]
[]
["Investigation"]
[null,"Description","text","Steady state studies for different oxygen availability in Escherichia coli"]
[null,"ID","integer","to create by SEEK"]
[null,"Comments","text"]
[]
["Study"]
[null,"Description","text","Determination of the impact of specific enzyme reactions and regulatory proteins using isogenic E. coli mutant strains"]
[null,"ID","integer","3.1.3"]
[null,"Type","text","chemostat"]
[null,"SOP","integer"]
[null,"Comments","text"]
[]
["Experiment"]
[null,"Description","text","chemostat-experiments at different aerobiosis levels (mixture of argon/air)"]
[null,"ID","integer","3.1.3.a"]
[null,"Type","text"]
[null,"SOP","integer","SUMO Evans medium","SUMO chemostat conditions"]
[null,"Comments"]
[null,"Culture_starting_date","date+time","24.06.08; 12.08.08; 17.03.09; 09.07.09"]
[]
["Assay"]
[null,"Description","text","mRNA expression rates","by-product formation rates","DCW-estimation","intracellular metabolites"]
[null,"ID","integer"]
[null,"Type","text","transcriptomics"]
[null,"SOP","integer","SUMO mRNA isolation Epicentre"]
[null,"Experimentalist","text","Sonja Steinsiek/Christine Richter","Sonja Steinsiek","Sonja Steinsiek","Stefan Stagge"]
[null,"Assay_date","date+time"]
[null,"Culture_age","time"]
[]
["Sampling"]
[null,"Type","text"]
[null,"SOP_sampling","integer"]
[null,"SOP_sample_preparation","integer","SUMO mRNA isolation Epicentre"]
[null,"User","integer","Sonja Steinsiek"]
[null,"Group","integer","Magdeburg"]
[]
[]
["ORGANISM"]
[null,"Organism ","integer","Escherichia coli K12"]
[null,"NCBI_ID","integer"]
[null,"Strain","text","MG1655"]
[null,"Genotype","text"]
[null,"Phenotype","text"]
[]
[]
["Experimental_conditions"]
[null,"Item","text","glucose","dilution rate",3,4,5,6]
[null,"SOP"]
[null,"Start_value","float/text",20,0.2]
[null,"End_value","float/text"]
[null,"Unit","text","mM","1/h"]
[null,"Comments","text"]
[]
["FACTORS_STUDIED"]
[null,"Factor","text","aeration"]
[null,"Start_value","float/text","0"]
[null,"End_value","float/text","100"]
[null,"Unit","text","%"]
[null,"action_time_point"]
[null,"Comments"]
[]
[]
["DATA_CREATED"]
[null,"Data_type","text"]
[null,"Status","text"]
[null,"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"]
[null,"Person_created","text","Sonja Steinsiek/Christine Richter"]
[]
["DATA_FILE"]
[null,"File_name","text"]
[null,"File_type","text","Excel sheets"]
[null,"Storage_location","text","local"]
[null,"Storage_date","date"]
[null,"Last_change_date","date"]
[null,"TemplateID","text","version 1"]
[]
["PUBLICATION"]
[null,"Title","text"]
[null,"Authors","text"]
[null,"Year","date"]
[null,"Journal","text"]
[null,"Volume","integer"]
[null,"Issue","integer"]
[null,"Pages","float"]
[null,"PubmedID","text"]
[null,"URL","text"]
[null,"DOI","float"]

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["Sample ID","chemostat_type","chemostat_ID","Experimentator ID","date",null,null,"aerobiosis","Code",null,"STRAIN","Genotype","SEEK Strain ID"]
[]
["sample_1","Multi",1,"SO","081212","_","%",0,"Multi1_SO081212_0%","2008-12-12","MG1655","wt",61]
["sample_2","Multi",1,"SO","090119","_","%",0,"Multi1_SO090119_0%","2009-01-19","MG1655","wt",61]
["sample_3","Multi",1,"SO","090213","_","%",0,"Multi1_SO090213_0%","2009-02-13","MG1655","wt",61]
["sample_4","Multi",1,"SO","090505","_","%",0,"Multi1_SO090505_0%","2009-05-05","MG1655","wt",61]
["sample_5","Multi",1,"SO","090714","_","%",0,"Multi1_SO090714_0%","2009-07-14","MG1655","wt",61]
["sample_6","Multi",1,"SO","100413","_","%",7.62,"Multi1_SO100413_7,62%","2010-04-13","MG1655","wt",61]
["sample_7","Multi",2,"SO","080610","_","%",20.18,"Multi2_SO080610_20,18%","2008-06-10","MG1655","wt",61]
["sample_8","Multi",4,"SO","081021","_","%",19.96,"Multi4_SO081021_19,96%","2008-10-21","MG1655","wt",61]
["sample_9","Multi",3,"SO","081111","_","%",19.96,"Multi3_SO081111_19,96%","2008-11-11","MG1655","wt",61]
["sample_10","Multi",2,"SO","080709","_","%",19.33,"Multi2_SO080709_19,33%","2008-07-09","MG1655","wt",61]
["sample_11","Multi",3,"SO","090303","_","%",20,"Multi3_SO090303_20%","2009-03-03","MG1655","wt",61]
["sample_12","Multi",2,"SO","090810","_","%",18.16,"Multi2_SO090810_18,16%","2009-08-10","MG1655","wt",61]
["sample_13","Multi",2,"SO","100504","_","%",38.79,"Multi2_SO100504_38,79%","2010-05-04","MG1655","wt",61]
["sample_14","Multi",2,"SO","100201","_","%",39.24,"Multi2_SO100201_39,24%","2010-02-01","MG1655","wt",61]
["sample_15","Multi",2,"SO","090112","_","%",50,"Multi2_SO090112_50%","2009-01-12","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%","2008-06-16","MG1655","wt",61]
["sample_18","Multi",1,"SO","090317","_","%",53.14,"Multi1_SO090317_53,14%","2009-03-17","MG1655","wt",61]
["sample_19","Multi",1,"SO","080618","_","%",79.6,"Multi1_SO080618_79,6%","2008-06-18","MG1655","wt",61]
["sample_20","Multi",1,"SO","090203","_","%",80.94,"Multi1_SO090203_80,94%","2009-02-03","MG1655","wt",61]
["sample_21","Multi",1,"SO","080812","_","%",78.48,"Multi1_SO080812_78,48%","2008-08-12","MG1655","wt",61]
["sample_22","Multi",1,"SO","080624","_","%",78.81,"Multi1_SO080624_78,81%","2008-06-24","MG1655","wt",61]
["sample_23","Multi",3,"SO","090303","_","%",84.08,"Multi3_SO090303_84,08%","2009-03-03","MG1655","wt",61]
["sample_24","Multi",2,"SO","091012","_","%",79.6,"Multi2_SO091012_79,6%","2009-10-12","MG1655","wt",61]
["sample_25","Multi",1,"SO","100208","_","%",95.29,"Multi1_SO100208_95,29%","2008-08-12","MG1655","wt",61]
["sample_26","Multi",2,"SO","100208","_","%",100.9,"Multi2_SO100208_100,9%","2008-06-24","MG1655","wt",61]
["sample_27","Multi",1,"SO","080812","_","%",98.65,"Multi1_SO080812_98,65%","2009-01-19","MG1655","wt",61]
["sample_28","Multi",3,"SO","080624","_","%",99.66,"Multi3_SO080624_99,66%","2009-03-17","MG1655","wt",61]
["sample_29","Multi",1,"SO","090119","_","%",100.22,"Multi1_SO090119_100,22%","2009-08-31","MG1655","wt",61]
["sample_30","Multi",3,"SO","090317","_","%",102.69,"Multi3_SO090317_102,69%","2010-02-08","MG1655","wt",61]
["sample_31","Multi",2,"SO","090831","_","%",101.46,"Multi2_SO090831_101,46%","2010-02-08","MG1655","wt",61]
["sample_32","Multi",3,"SO","090310","_","%",120.85,"Multi3_SO090310_120,85%","2009-03-10","MG1655","wt",61]
["sample_33","Multi",3,"SO","091218","_","%",118.83,"Multi3_SO091218_118,83%","2009-12-18","MG1655","wt",61]
["sample_34","Multi",4,"SO","091218","_","%",121.52,"Multi4_SO091218_121,52%","2009-12-18","MG1655","wt",61]

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["Parameters of bioreactor"]
[null,"Parameter","Value","Units","Comments"]
[null,"pO2",null,"%","oxygenation"]
[null,"V_reactor",1,"L","overall reactor volume"]
[null,"V_tot",0.36,"L","total reaction volume (or working volume of broth that includes both extra- and intracellular volumes)"]
[null,"D",0.2,"h-1","dilution rate"]
[null,"r_gas",0.18,"L/min","gas inflow"]
[null,"r_feed",1.2,"mL/min","rate of feeding"]
[null,"C_glc_feed",20,"mmol/L","glucose concentration in feed"]
[null,"T",37,"°C","operation temperature"]
[null,"pH",6.9,null,"operation pH"]
[null,"stirring",550,"rpm","stirring rate"]
[null,"r_gas",0.18,"L/min","gas flow rate"]
[]
[null,"C_x",null,"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,null,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,null,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]