{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000173","ANALYSIS_ID":"AN000267","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Evolutionary-genomics approach for elucidating and improving complex phenotypes","PROJECT_SUMMARY":"Genome evolution and engineering to study isobutanol tolerance in E. coli","INSTITUTE":"University of Michigan","DEPARTMENT":"Chemical Engineering","LABORATORY":"Lin Lab","LAST_NAME":"Lin","FIRST_NAME":"Nina","ADDRESS":"Ann Arbor, MI","EMAIL":"ninalin@umich.edu","PHONE":"734-647-8026"},

"STUDY":{"STUDY_TITLE":"WT and iButOH tolerant E. coli","STUDY_TYPE":"Comparative metabolomics study of WT and iButOH tolerant E. coli","STUDY_SUMMARY":"This study aims to elucidate metabolic mechanisms of tolerance to isobutanol in coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol strain 38-20-4 created via multiplex genome engineering. The metabolic response growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media be compared for each strain. 3 replicates for each strain/iButOH concentration been submitted, excpet for WT/0.7%; we have observed high growth phenotype for this combination, and have corresponding submitted 5x replicates. Strain contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises rewiring of TCA cycle and amino acid metabolism, possibly resulting in intracellular ratio of glutamine:glutamate","INSTITUTE":"University of Michigan","DEPARTMENT":"Biomedical Research Core Facilities","LABORATORY":"Metabolomics core","LAST_NAME":"Kachman","FIRST_NAME":"Maureen","ADDRESS":"6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714","EMAIL":"mkachman@umich.edu","PHONE":"-","NUM_GROUPS":"4","TOTAL_SUBJECTS":"14"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"SU0003750",
"Sample ID":"S00014363",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003750",
"Sample ID":"S00014364",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003750",
"Sample ID":"S00014365",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003751",
"Sample ID":"S00014369",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0% (w/v)"}
},
{
"Subject ID":"SU0003751",
"Sample ID":"S00014370",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0% (w/v)"}
},
{
"Subject ID":"SU0003751",
"Sample ID":"S00014371",
"Factors":{"Strain":"iButOH tol mutant","iButOH concentration":"0% (w/v)"}
},
{
"Subject ID":"SU0003749",
"Sample ID":"S00014358",
"Factors":{"Strain":"WT","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003749",
"Sample ID":"S00014359",
"Factors":{"Strain":"WT","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003749",
"Sample ID":"S00014360",
"Factors":{"Strain":"WT","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003749",
"Sample ID":"S00014361",
"Factors":{"Strain":"WT","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003749",
"Sample ID":"S00014362",
"Factors":{"Strain":"WT","iButOH concentration":"0.7% (w/v)"}
},
{
"Subject ID":"SU0003750",
"Sample ID":"S00014366",
"Factors":{"Strain":"WT","iButOH concentration":"0% (w/v)"}
},
{
"Subject ID":"SU0003750",
"Sample ID":"S00014367",
"Factors":{"Strain":"WT","iButOH concentration":"0% (w/v)"}
},
{
"Subject ID":"SU0003750",
"Sample ID":"S00014368",
"Factors":{"Strain":"WT","iButOH concentration":"0% (w/v)"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"-"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_FILENAME":"Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1260","COLUMN_NAME":"Phenomenex Luna NH2 (150 x 1mm, 3um)","METHODS_ID":"AQM020","METHODS_FILENAME":"QTOF-002-HILIC-35min-1mm-No_Insert.m.zip"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"MRC2 (University of Michigan)","ACQUISITION_PARAMETERS_FILE":"QTOF-002-HILIC-35min-1mm-No_Insert.m.zip","PROCESSING_PARAMETERS_FILE":"EX00268-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m.zip"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6520 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"pmol/µg protein",

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}

}