{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000884","ANALYSIS_ID":"AN001441","VERSION":"1","CREATED_ON":"October 30, 2017, 5:23 pm"},

"PROJECT":{"PROJECT_TITLE":"Evidence that COG0325 proteins are involved in Pyridoxal 5'-phosphate (PLP) homeostasis","PROJECT_SUMMARY":"Pyridoxal 5'-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.","INSTITUTE":"University of Florida","DEPARTMENT":"Microbiology and Cell Science","LAST_NAME":"de Crecy-Lagard","FIRST_NAME":"Valerie","ADDRESS":"Gainesville, FL 32611","EMAIL":"vcrecy@ufl.edu","PHONE":"352-392-9416"},

"STUDY":{"STUDY_TITLE":"Evidence that COG0325 proteins are involved in PLP homeostasis","STUDY_SUMMARY":"Pyridoxal 5'-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","STUDY_COMMENTS":"LB stands for Luria Bertani medium. MG stands for minimal growth For strains grown on MG OD 0.5 is the mid log growth phase and OD 1.0 is the late log growth phase For strains grown on LB OD 1 is the mid log growth phase and OD 2.0 is the late log growth phase"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"LB1 #1",
"Sample ID":"150706bctsa06_3",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #1",
"Sample ID":"150706bctsa15_3",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #1",
"Sample ID":"150706bctsa01_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #1",
"Sample ID":"150708bctsa15_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #1",
"Sample ID":"150706bctsa44_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #1",
"Sample ID":"150707bctsa37_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB1 #2",
"Sample ID":"150708bctsa35_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #2",
"Sample ID":"150708bctsa24_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #2",
"Sample ID":"150706bctsa40_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #2",
"Sample ID":"150706bctsa37_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #2",
"Sample ID":"150706bctsa28_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150706bctsa48_3",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150706bctsa05_3",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150708bctsa12_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150707bctsa38_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150707bctsa42_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150707bctsa16_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150707bctsa30_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150708bctsa27_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150708bctsa47_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150706bctsa24_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #4",
"Sample ID":"150709bctsa06_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150708bctsa06_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150707bctsa48_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150708bctsa48_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150706bctsa29_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150707bctsa36_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #7",
"Sample ID":"150707bctsa01_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150708bctsa01_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150707bctsa41_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150707bctsa25_1",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150706bctsa03_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150706bctsa19_3",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB1 #8",
"Sample ID":"150706bctsa42_2",
"Factors":{"Treatment":"LB OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150708bctsa44_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150708bctsa19_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150707bctsa33_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150706bctsa49_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150706bctsa10_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #1",
"Sample ID":"150706bctsa08_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150707bctsa23_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150707bctsa24_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150707bctsa34_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB1 #3",
"Sample ID":"150708bctsa07_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150706bctsa45_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150706bctsa47_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #2",
"Sample ID":"150707bctsa13_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150706bctsa12_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150706bctsa13_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150706bctsa23_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150707bctsa03_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150707bctsa14_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #3",
"Sample ID":"150707bctsa28_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150708bctsa50_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150708bctsa45_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150708bctsa20_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150708bctsa04_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150706bctsa18_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #4",
"Sample ID":"150706bctsa02_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150706bctsa41_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150706bctsa22_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150707bctsa27_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150707bctsa06_3",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150709bctsa10_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #7",
"Sample ID":"150707bctsa43_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150706bctsa07_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150707bctsa10_3",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150706bctsa09_3",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150707bctsa26_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150707bctsa49_2",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB2 #8",
"Sample ID":"150708bctsa46_1",
"Factors":{"Treatment":"LB OD 2.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #1",
"Sample ID":"150706bctsa26_2",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.5 #1",
"Sample ID":"150706bctsa35_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.5 #1",
"Sample ID":"150707bctsa12_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.5 #1",
"Sample ID":"150708bctsa18_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.5 #1",
"Sample ID":"150708bctsa42_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150708bctsa08_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150708bctsa30_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150707bctsa39_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150707bctsa44_2",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150707bctsa05_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #2",
"Sample ID":"150708bctsa34_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150706bctsa39_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150706bctsa46_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150706bctsa43_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150707bctsa35_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150706bctsa50_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #3",
"Sample ID":"150707bctsa50_2",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.5 #4",
"Sample ID":"150707bctsa07_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.5 #4",
"Sample ID":"150708bctsa03_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.5 #4",
"Sample ID":"150707bctsa21_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.5 #4",
"Sample ID":"150708bctsa43_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.5 #4",
"Sample ID":"150708bctsa26_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150708bctsa02_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150706bctsa14_3",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150709bctsa07_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150708bctsa22_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150708bctsa14_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #5",
"Sample ID":"150708bctsa05_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150706bctsa20_3",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150708bctsa41_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150707bctsa19_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150708bctsa28_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150707bctsa04_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #7",
"Sample ID":"150707bctsa18_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150709bctsa05_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150708bctsa31_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150707bctsa45_2",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150708bctsa39_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150708bctsa37_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG0.5 #8",
"Sample ID":"150706bctsa32_1",
"Factors":{"Treatment":"MG OD 0.5","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #1",
"Sample ID":"150709bctsa09_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG1 #1",
"Sample ID":"150707bctsa08_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG1 #1",
"Sample ID":"150707bctsa32_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG1 #1",
"Sample ID":"150708bctsa49_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG1 #1",
"Sample ID":"150706bctsa16_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150709bctsa02_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150706bctsa17_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150707bctsa29_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150708bctsa36_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150707bctsa17_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.7 #2",
"Sample ID":"150707bctsa20_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG0.8 #3",
"Sample ID":"150709bctsa04_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.8 #3",
"Sample ID":"150708bctsa23_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.8 #3",
"Sample ID":"150706bctsa11_3",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.8 #3",
"Sample ID":"150708bctsa10_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.8 #3",
"Sample ID":"150707bctsa02_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG0.8 #4",
"Sample ID":"150708bctsa40_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.8 #4",
"Sample ID":"150708bctsa09_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.8 #4",
"Sample ID":"150709bctsa11_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.8 #4",
"Sample ID":"150707bctsa46_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG0.8 #4",
"Sample ID":"150707bctsa11_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG1 #5",
"Sample ID":"150707bctsa47_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG1 #5",
"Sample ID":"150706bctsa04_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG1 #5",
"Sample ID":"150708bctsa21_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG1 #5",
"Sample ID":"150708bctsa25_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG1 #5",
"Sample ID":"150708bctsa29_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG1 #7",
"Sample ID":"150708bctsa16_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG1 #7",
"Sample ID":"150707bctsa40_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG1 #7",
"Sample ID":"150709bctsa03_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG1 #7",
"Sample ID":"150708bctsa32_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150708bctsa17_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150708bctsa11_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150708bctsa13_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150707bctsa09_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150707bctsa31_1",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG1 #8",
"Sample ID":"150706bctsa27_2",
"Factors":{"Treatment":"MG OD 1.0","SampleType":"Cell Pellets","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB SN #1",
"Sample ID":"150624bctsa06_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB SN 1.0  #2A",
"Sample ID":"150624bctsa02_4",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 1.0 #2B",
"Sample ID":"150624bctsa08_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 1.0 #3",
"Sample ID":"150624bctsa09_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB SN 1.0 #4",
"Sample ID":"150624bctsa10_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB SN 1.0 #7B",
"Sample ID":"150624bctsa03_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB SN 1.0 #8B",
"Sample ID":"150624bctsa11_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB SN #2",
"Sample ID":"150624bctsa07_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 2.0 #2",
"Sample ID":"150624bctsa01_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 2.0 #3",
"Sample ID":"150624bctsa05_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB SN 2.0 #4",
"Sample ID":"150624bctsa12_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB SN 2.0 #7",
"Sample ID":"150624bctsa13_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB SN 2.0 #8B",
"Sample ID":"150624bctsa04_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB SN 1.0 #2",
"Sample ID":"150623bctsa28_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 1.0 #7",
"Sample ID":"150623bctsa18_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB SN 1.0 #4",
"Sample ID":"150623bctsa10_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"LB SN 1.0 #1",
"Sample ID":"150623bctsa05_4",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"LB SN 1.0 #8",
"Sample ID":"150623bctsa17_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB SN 1.0 #3",
"Sample ID":"150623bctsa15_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"LB SN 2.0 #8",
"Sample ID":"150623bctsa16_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"LB SN 2.0 #3",
"Sample ID":"150623bctsa08_2",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 2.0 #2",
"Sample ID":"150623bctsa26_1",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"LB SN 2.0 #7",
"Sample ID":"150623bctsa06_4",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"LB SN 2.0 #4",
"Sample ID":"150623bctsa03_3",
"Factors":{"Treatment":"LB Supernatant (SN) OD 2.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG SN 0.5 #8",
"Sample ID":"150623bctsa25_1",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone 2)"}
},
{
"Subject ID":"MG SN 0.5 #5",
"Sample ID":"150623bctsa24_1",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
},
{
"Subject ID":"MG SN 0.5 #7",
"Sample ID":"150623bctsa19_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG SN 0.5 #2",
"Sample ID":"150623bctsa07_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG SN 0.5 #1",
"Sample ID":"150623bctsa02_3",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG SN 0.5 #4",
"Sample ID":"150623bctsa01_3",
"Factors":{"Treatment":"MG Supernatant (SN) OD 0.5","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG SN 1.0 #1",
"Sample ID":"150623bctsa27_1",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6594)"}
},
{
"Subject ID":"MG SN 1.0 #3",
"Sample ID":"150623bctsa22_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA (strain VDC6664)"}
},
{
"Subject ID":"MG SN 1.0 #7",
"Sample ID":"150623bctsa14_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli WT BW25113 (clone1)"}
},
{
"Subject ID":"MG SN 1.0 #4",
"Sample ID":"150623bctsa13_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta glyA  (strain​ VDC6665)"}
},
{
"Subject ID":"MG SN 1.0 #2",
"Sample ID":"150623bctsa04_4",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli Delta yggS (strain VDC6595)"}
},
{
"Subject ID":"MG SN 1.0 #5",
"Sample ID":"150623bctsa11_2",
"Factors":{"Treatment":"MG Supernatant (SN) OD 1.0","SampleType":"extracellular supernatant","Strain":"E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were grown overnight in M9 glucose 0.2% (w/v) supplemented with 1 mM glycine at 37 °C, and then were diluted to an OD of 0.03 in M9 glucose 0.2% (w/v) supplemented with 1 mM glycine. Mid-log (OD600=0.5) or late-log (OD600=1) samples were centrifuged for 20 s at 13,500 g and stored at -80 °C.","SAMPLE_TYPE":"Cell"},

"TREATMENT":{"TREATMENT_SUMMARY":"Bacteria were grown on Luria Bertani (LB) medium (BD Diagnostics Systems) at 37°C or on M9 minimal medium supplemented with 0.2 % (w/v) glucose and 1 mM glycine"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"B6 species [PLP, PNP, pyridoxamine 5'-phosphate (PMP), PL, PN and PM] were extracted from WT and ΔyggS pellets (1.0 ml culture of OD60051.0) in 0.9 ml 5 % (w/v) metaphosphoric acid and 0.1 ml internal standard 4-deoxypyridoxine (73 nmol/ml in 5 % metaphosphoric acid). The suspension was vortexed and sonicated. After centrifugation at 10 000 g for 15 min, the supernatant was filtered and a 50 ml sample was taken for HPLC analysis using fluorescence detection (excitation 328 nm, emission 393 nm)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um) 0.25 μm film made of 95% dimethyl/5%diphenylpolysiloxane)","FLOW_RATE":"1 ml/min","COLUMN_TEMPERATURE":"50 - 330°C","COLUMN_PRESSURE":"7.7 PSI (initial condition)","INJECTION_TEMPERATURE":"50°C ramped to 250°C by 12°C/s","SAMPLE_INJECTION":"0.5 uL","OVEN_TEMPERATURE":"50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min","TRANSFERLINE_TEMPERATURE":"230°C","WASHING_BUFFER":"Ethyl Acetate","SAMPLE_LOOP_SIZE":"30 m length x 0.25 mm internal diameter","RANDOMIZATION_ORDER":"Excel generated"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","DETECTOR_TYPE":"TOF","SOFTWARE_VERSION":"Chromatof","DATA_FORMAT":".netcdf"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Leco Pegasus III GC TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","ION_SOURCE_TEMPERATURE":"250°C","IONIZATION_ENERGY":"70eV","MASS_ACCURACY":"Nominal","SCAN_RANGE_MOVERZ":"85-500","SCANNING_CYCLE":"17 Hz","SCANNING_RANGE":"80-500 Da","SKIMMER_VOLTAGE":"1850","MS_RESULTS_FILE":"ST000884_AN001441_Results.txt UNITS:Counts"},

"MS_METABOLITE_DATA":{
"Units":"Counts",

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