{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001421","ANALYSIS_ID":"AN002376","VERSION":"1","CREATED_ON":"July 10, 2020, 1:50 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic analysis of Escherichia coli K-12 MG1655 transcriptional regulator mutants under anaerobic conditions","PROJECT_TYPE":"Metabolomics","PROJECT_SUMMARY":"Metabolomic analysis of Wildtype, fnr, arcA and ihf mutants in glucose minimal media under anaerobic fermentation conditions during its exponential phase of growth. Three biological and two technical replicates samples (n=6) were harvested for each of the strains while growing in a bioreactor anaerobically at 37 degrees Celsius and 150 rpm. This study aims to characterize and compare the metabolic profiles of all these strains.","INSTITUTE":"IIT Bombay","DEPARTMENT":"Department of Chemical Engineering","LABORATORY":"Systems Biology and Metabolic Engineering Laboratory","LAST_NAME":"Pal","FIRST_NAME":"Ankita","ADDRESS":"Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076, India","EMAIL":"pal.ankita90@gmail.com","PHONE":"08879536816"},

"STUDY":{"STUDY_TITLE":"Metabolomic study of Escherichia coli K-12 MG1655 WT and its transcriptional regulator mutants under anaerobic fermentation conditions","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"Metabolomic analysis of Wildtype, fnr, arcA and ihf mutants in glucose minimal media under anaerobic fermentation conditions during its exponential phase of growth. Three biological and two technical replicate samples (n=6) were harvested for each of the strains while growing in a bioreactor anaerobically at 37 degrees Celsius and 150 rpm. This study aims to characterize and compare the metabolic profiles of all these strains.","INSTITUTE":"IIT Bombay","DEPARTMENT":"Department of Chemical Engineering","LABORATORY":"Systems Biology and Metabolic Engineering Laboratory (SBMEL)","LAST_NAME":"Pal","FIRST_NAME":"Ankita","ADDRESS":"Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076, India","EMAIL":"pal.ankita90@gmail.com","PHONE":"08879536816"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562","GENOTYPE_STRAIN":"K-12 MG1655"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Wild-type_1",
"Sample ID":"WT_1",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_1.RAW;WT_negative_1.RAW"}
},
{
"Subject ID":"Wild-type_2",
"Sample ID":"WT_2",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_2.RAW;WT_negative_2.RAW"}
},
{
"Subject ID":"Wild-type_3",
"Sample ID":"WT_3",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_3.RAW;WT_negative_3.RAW"}
},
{
"Subject ID":"Wild-type_4",
"Sample ID":"WT_4",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_4.RAW;WT_negative_4.RAW"}
},
{
"Subject ID":"Wild-type_5",
"Sample ID":"WT_5",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_5.RAW;WT_negative_5.RAW"}
},
{
"Subject ID":"Wild-type_6",
"Sample ID":"WT_6",
"Factors":{"Genotype":"Wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"WT_positive_6.RAW;WT_negative_6.RAW"}
},
{
"Subject ID":"FNR-knockout_1",
"Sample ID":"FNR_1",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_1.RAW;FNR_negative_1.RAW"}
},
{
"Subject ID":"FNR-knockout_2",
"Sample ID":"FNR_2",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_2.RAW;FNR_negative_2.RAW"}
},
{
"Subject ID":"FNR-knockout_3",
"Sample ID":"FNR_3",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_3.RAW;FNR_negative_3.RAW"}
},
{
"Subject ID":"FNR-knockout_4",
"Sample ID":"FNR_4",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_4.RAW;FNR_negative_4.RAW"}
},
{
"Subject ID":"FNR-knockout_5",
"Sample ID":"FNR_5",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_5.RAW;FNR_negative_5.RAW"}
},
{
"Subject ID":"FNR-knockout_6",
"Sample ID":"FNR_6",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"FNR_positive_6.RAW;FNR_negative_6.RAW"}
},
{
"Subject ID":"ArcA-knockout_1",
"Sample ID":"ArcA_1",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_1.RAW;ArcA_negative_1.RAW"}
},
{
"Subject ID":"ArcA-knockout_2",
"Sample ID":"ArcA_2",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_2.RAW;ArcA_negative_2.RAW"}
},
{
"Subject ID":"ArcA-knockout_3",
"Sample ID":"ArcA_3",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_3.RAW;ArcA_negative_3.RAW"}
},
{
"Subject ID":"ArcA-knockout_4",
"Sample ID":"ArcA_4",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_4.RAW;ArcA_negative_4.RAW"}
},
{
"Subject ID":"ArcA-knockout_5",
"Sample ID":"ArcA_5",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_5.RAW;ArcA_negative_5.RAW"}
},
{
"Subject ID":"ArcA-knockout_6",
"Sample ID":"ArcA_6",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"ArcA_positive_6.RAW;ArcA_negative_6.RAW"}
},
{
"Subject ID":"IHF-knockout_1",
"Sample ID":"IHF_1",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_1.RAW;IHF_negative_1.RAW"}
},
{
"Subject ID":"IHF-knockout_2",
"Sample ID":"IHF_2",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_2.RAW;IHF_negative_2.RAW"}
},
{
"Subject ID":"IHF-knockout_3",
"Sample ID":"IHF_3",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_3.RAW;IHF_negative_3.RAW"}
},
{
"Subject ID":"IHF-knockout_4",
"Sample ID":"IHF_4",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_4.RAW;IHF_negative_4.RAW"}
},
{
"Subject ID":"IHF-knockout_5",
"Sample ID":"IHF_5",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_5.RAW;IHF_negative_5.RAW"}
},
{
"Subject ID":"IHF-knockout_6",
"Sample ID":"IHF_6",
"Factors":{"Genotype":"Mutant"},
"Additional sample data":{"RAW_FILE_NAME":"IHF_positive_6.RAW;IHF_negative_6.RAW"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The WT, fnr, arcA and ihf mutants were grown in a bioreactor in glucose minimal media under anaerobic fermentation conditions at 37 degrees Celsius and 150 rpm. The samples were harvested during its exponential phase of growth for three biological and two technical replicates (n=6). The metabolites were extracted using the Methanol-Chloroform-Water method. Detailed sample collection protocol is described in “Extraction_protocol_msi.pdf”.","COLLECTION_PROTOCOL_FILENAME":"Extraction_protocol_msi.pdf","SAMPLE_TYPE":"Bacterial cells","COLLECTION_METHOD":"Methanol-Chloroform-Water method","COLLECTION_LOCATION":"IIT Bombay, Powai, Mumbai- 400076, Mumbai, Maharashtra","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"The WT, fnr, arcA and ihf mutants were grown in a bioreactor in glucose minimal media under anaerobic fermentation conditions at 37 degrees Celsius and 150 rpm. The samples were harvested during its exponential phase of growth for three biological and two technical replicates (n=6). The metabolites were extracted using the Methanol-Chloroform-Water method.","CELL_GROWTH_CONTAINER":"Bioreactor","CELL_MEDIA":"M9 + Glucose","CELL_ENVIR_COND":"37 degrees Celsius, 150 rpm. anaerobic fermentation"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples were extracted from the Wildtype, fnr, arcA and ihf mutants grown in a bioreactor anaerobically in glucose minimal media at 37 degrees Celsius and 150 rpm. The metabolites were extracted using the Methanol-Chloroform-Water method. The samples were spiked with an equal volume of 13C-labelled internal standard taken from the same batch at an earlier stage to prevent to account for losses due to metabolite degradation and to enable robust quantification circumventing the ion-suppression effects.","SAMPLEPREP_PROTOCOL_FILENAME":"MS-method_msi.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The detailed chromatography and MS protocol has been described in MS-method_msi.pdf file.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)","METHODS_FILENAME":"MS-method_msi.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Data acquisition done using parent ion MS intensities. Peak height used for processing. Xcalibur 4.3.73.11 used for data analysis and peak integration. Missing value imputation was done using SVD impute function in MetaboAnalyst."},

"MS_METABOLITE_DATA":{
"Units":"umol/gDCW",

"Data":[{"Metabolite":"Leucine","WT_1":"4.339392777","WT_2":"4.071342108","WT_3":"4.596626868","WT_4":"4.595376637","WT_5":"5.52","WT_6":"5.18","FNR_1":"6.400957329","FNR_2":"10.46297463","FNR_3":"8.317017177","FNR_4":"6.815287827","FNR_5":"8.507162434","FNR_6":"6.62992152","ArcA_1":"3.498277807","ArcA_2":"5.15511304","ArcA_3":"6.236686214","ArcA_4":"3.470223217","ArcA_5":"6.011367319","ArcA_6":"3.353149384","IHF_1":"10.78442774","IHF_2":"9.899176408","IHF_3":"8.171941777","IHF_4":"7.636763439","IHF_5":"8.061992735","IHF_6":"7.310259808"},{"Metabolite":"Phenylalanine","WT_1":"0.663109999","WT_2":"0.656541175","WT_3":"0.631053559","WT_4":"0.631705113","WT_5":"0.73","WT_6":"0.97","FNR_1":"0.960255482","FNR_2":"1.832949007","FNR_3":"0.470839972","FNR_4":"0.482867824","FNR_5":"0.455445593","FNR_6":"0.446287823","ArcA_1":"0.919374719","ArcA_2":"1.078995121","ArcA_3":"0.350754917","ArcA_4":"0.28562148","ArcA_5":"0.337612049","ArcA_6":"0.269234839","IHF_1":"1.278624674","IHF_2":"1.651430028","IHF_3":"0.392353579","IHF_4":"0.416453329","IHF_5":"0.378744908","IHF_6":"0.405724361"},{"Metabolite":"Methionine","WT_1":"1.71898291","WT_2":"1.653582903","WT_3":"1.962846801","WT_4":"2.00167123","WT_5":"1.93","WT_6":"2.15","FNR_1":"2.284351434","FNR_2":"3.177159331","FNR_3":"2.243830731","FNR_4":"2.075451872","FNR_5":"2.241108933","FNR_6":"2.050252508","ArcA_1":"2.245156179","ArcA_2":"3.435884253","ArcA_3":"2.92447345","ArcA_4":"2.247891346","ArcA_5":"2.689877845","ArcA_6":"2.210463807","IHF_1":"3.714671528","IHF_2":"4.467733801","IHF_3":"2.848516825","IHF_4":"2.608039959","IHF_5":"2.819914201","IHF_6":"2.546690231"},{"Metabolite":"Tryptophan","WT_1":"0.133562342","WT_2":"0.135524122","WT_3":"0.13148099","WT_4":"0.130893034","WT_5":"0.13","WT_6":"0.2","FNR_1":"0.155114099","FNR_2":"0.163983263","FNR_3":"0.134010529","FNR_4":"0.133309635","FNR_5":"0.130628621","FNR_6":"0.120272303","ArcA_1":"0.149292103","ArcA_2":"0.160557927","ArcA_3":"0.071185928","ArcA_4":"0.082106401","ArcA_5":"0.066810792","ArcA_6":"0.077600612","IHF_1":"0.335915592","IHF_2":"0.329427835","IHF_3":"0.151157441","IHF_4":"0.137912775","IHF_5":"0.140411937","IHF_6":"0.127793229"},{"Metabolite":"Proline","WT_1":"0.596864506","WT_2":"0.584915861","WT_3":"1.104842009","WT_4":"1.0868342","WT_5":"1.27","WT_6":"0.88","FNR_1":"2.197420349","FNR_2":"2.758159229","FNR_3":"1.129651175","FNR_4":"0.931316217","FNR_5":"1.035418475","FNR_6":"0.90061166","ArcA_1":"1.317195749","ArcA_2":"2.200637938","ArcA_3":"1.537510458","ArcA_4":"0.732046502","ArcA_5":"1.502324713","ArcA_6":"0.71257337","IHF_1":"2.632512824","IHF_2":"2.575394694","IHF_3":"2.155921224","IHF_4":"1.764593228","IHF_5":"2.086671525","IHF_6":"1.73153624"},{"Metabolite":"Valine","WT_1":"5.386763361","WT_2":"3.10520573","WT_3":"5.572423982","WT_4":"5.628870515","WT_5":"8.29","WT_6":"4.63","FNR_1":"7.59487846","FNR_2":"11.24208446","FNR_3":"17.04611781","FNR_4":"11.00740305","FNR_5":"16.65561849","FNR_6":"10.72153007","ArcA_1":"3.300576121","ArcA_2":"5.776501569","ArcA_3":"9.57817371","ArcA_4":"4.482262381","ArcA_5":"12.54724314","ArcA_6":"4.224681834","IHF_1":"8.082713656","IHF_2":"7.263760513","IHF_3":"9.240514947","IHF_4":"8.029229587","IHF_5":"15.17189956","IHF_6":"7.670512912"},{"Metabolite":"Tyrosine","WT_1":"1.18408796","WT_2":"1.198604713","WT_3":"1.846440277","WT_4":"1.95226411","WT_5":"2.85","WT_6":"1.6","FNR_1":"1.26395932","FNR_2":"3.809440995","FNR_3":"2.884604697","FNR_4":"2.587744294","FNR_5":"2.809217948","FNR_6":"2.668907596","ArcA_1":"1.151714143","ArcA_2":"1.629195913","ArcA_3":"1.637825939","ArcA_4":"1.130908024","ArcA_5":"1.563744573","ArcA_6":"1.146346172","IHF_1":"1.986286571","IHF_2":"2.375440091","IHF_3":"1.661753456","IHF_4":"1.871655559","IHF_5":"1.503531392","IHF_6":"1.739794669"},{"Metabolite":"Alanine","WT_1":"23.53978108","WT_2":"23.7608482","WT_3":"39.23017769","WT_4":"38.38480395","WT_5":"44.64","WT_6":"33.01","FNR_1":"43.7836075","FNR_2":"71.02241188","FNR_3":"43.90196622","FNR_4":"32.13580673","FNR_5":"47.8771668","FNR_6":"34.36020668","ArcA_1":"26.34104268","ArcA_2":"59.8208647","ArcA_3":"32.36534191","ArcA_4":"18.00789491","ArcA_5":"34.09081958","ArcA_6":"18.71218693","IHF_1":"65.5102225","IHF_2":"64.05751276","IHF_3":"34.81014983","IHF_4":"32.95545951","IHF_5":"34.92097713","IHF_6":"33.12270166"},{"Metabolite":"Threonine","WT_1":"2.163773106","WT_2":"2.197844239","WT_3":"2.695540594","WT_4":"2.679859374","WT_5":"3.31","WT_6":"2.69","FNR_1":"4.011864681","FNR_2":"4.129708141","FNR_3":"7.236579635","FNR_4":"6.299573039","FNR_5":"6.805043381","FNR_6":"5.956167302","ArcA_1":"2.126623086","ArcA_2":"3.233085166","ArcA_3":"4.331037788","ArcA_4":"2.624980014","ArcA_5":"4.148659664","ArcA_6":"2.52664784","IHF_1":"6.47694215","IHF_2":"7.198727943","IHF_3":"7.912591471","IHF_4":"7.36602894","IHF_5":"7.646783705","IHF_6":"6.839066035"},{"Metabolite":"Histidine","WT_1":"0.6430585","WT_2":"0.642164429","WT_3":"0.976755049","WT_4":"1.091947178","WT_5":"1.244768712","WT_6":"0.887764829","FN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}

}