{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000973","ANALYSIS_ID":"AN001594","VERSION":"1","CREATED_ON":"May 24, 2018, 2:12 pm"},

"PROJECT":{"PROJECT_TITLE":"Identification of biomarkers in schistosomiasis and associated bladder cancer and pathologies in Eggua, Nigeria","PROJECT_SUMMARY":"The aim of the project is to develop biomarkers that will aid the search for new therapeutic or diagnostic targets for schistosomiasis and its induced bladder pathologies or cancer. Blood and urine samples from individuals were collected in Eggua, Nigeria for subsequent metabolomics, proteomics and genomics characterization","INSTITUTE":"University of Ibadan, Nigeria","DEPARTMENT":"Zoology (Cell biology and Genetics unit)","LABORATORY":"Centre for Materials Characterization, National Chemical Laboratory, Pune, India","LAST_NAME":"Adewale","FIRST_NAME":"Adebayo","ADDRESS":"Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India","EMAIL":"walsaks@gmail.com","PHONE":"07030710368"},

"STUDY":{"STUDY_TITLE":"Metabolome profiles in urogenital schistosomiasis and associated pathologies (part II)","STUDY_SUMMARY":"Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were collected from volunteers in Eggua community, Nigeria, after ethical approval. LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools were used to detect important metabolites","INSTITUTE":"University of Ibadan, Nigeria","DEPARTMENT":"Zoology (Cell biology and Genetics unit)","LABORATORY":"Centre for Materials Characterization, National Chemical Laboratory, Pune, India","LAST_NAME":"Adebayo","FIRST_NAME":"Adewale","ADDRESS":"Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India","EMAIL":"walsaks@gmail.com","PHONE":"07030710368"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","HUMAN_ETHNICITY":"Yoruba","HUMAN_INCLUSION_CRITERIA":"apparent health, no recent treatment for any disease, no recent use of antibiotics, antimalarial or other drugs"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-0041",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-0042",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-0043",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-161",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-162",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-163",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-221",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-222",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-223",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-391",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-392",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-393",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-401",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-402",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-403",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-461",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-462",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-463",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-851",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-852",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-853",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-1041",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-1042",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"S-1043",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"PLASMA","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-41",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-42",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-43",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-161",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-162",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-163",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-221",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-222",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-223",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-391",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-392",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-393",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-401",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-402",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-403",
"Factors":{"Status":"CONTROL","Stage":"CONTROL"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-461",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-462",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-463",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-851",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-852",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-853",
"Factors":{"Status":"INFECTED","Stage":"INFECTION-ONLY"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-1041",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-1042",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
},
{
"Subject ID":"HOMO SAPIENS",
"Sample ID":"U-1043",
"Factors":{"Status":"INFECTED","Stage":"ADVANCED"},
"Additional sample data":{"SAMPLE_TYPE":"URINE","IONISATION":"POSITIVE"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"blood and urine samples collected from volunteers in the morning hours. Plasma was separated from blood. urine was examined for S. haematobium infection. Distended Bladder scans were carried out","COLLECTION_PROTOCOL_ID":"UI/EC/15/0019","SAMPLE_TYPE":"Plasma;Urine"},

"TREATMENT":{"TREATMENT_SUMMARY":"Samples were categorised as infected, infected with pathologies, and controls. Infection with Schistosoma haematobium infection by examining urine under the microscopy to detect eggs and by amplifying Dra 1 region. Pathologies were determined ultrasonography"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Both urine and plasma samples were prepared using chilled methanol:water mixture (4:1)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Both urine and plasma samples were prepared using chilled methanol:water mixture (4:1). Separation was achieved with 150mm x 2.1mm, 1.9μ Hypersil Gold column with a 5μl injection volume. Gradient elution was performed using 0.1% formic acid in water (A) and acetonitrile (B) as mobile phase after optimization. The column was washed between each sample for stability and to eliminate carry-over. The flow rate was 0.35 ml/min. MS acquisition was performed on the Q-Exactive hybrid quadrupole orbitrap mass spectrometer (ThermoFisher, MA, USA) operated in positive and negative electrospray ionization (ESI) modes. The scan range was 70 to 1000 m/z.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Q-Exactive hybrid quadrupole orbitrap mass spectrometer","COLUMN_NAME":"Hypersil Gold column"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"National Chemical Laboratory, Pune, India"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_RESULTS_FILE":"ST000973_AN001594_Results.txt UNITS:abundance of specific m/z (amu)"}

}