Summary of Study ST000934

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000646. The data can be accessed directly via it's Project DOI: 10.21228/M85M3S This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000934
Study TitleMetabolome profiles in urogenital schistosomiasis and associated pathologies
Study SummaryMetabolic 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
DepartmentZoology (Cell biology and Genetics unit)
LaboratoryCentre for Materials Characterization, National Chemical Laboratory, Pune, India
Last NameAdewale
First NameAdebayo
AddressCell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India
Emailwalsaks@gmail.com
Phone07030710368
Submit Date2017-12-02
Publicationsdoi:10.1371/journal.pntd.0006452
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Adebayo Adewale Adebayo Adewale
https://dx.doi.org/10.21228/M85M3S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000646
Project DOI:doi: 10.21228/M85M3S
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

Subject:

Subject ID:SU000973
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
Species Group:Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Status Stage
SA055616S-402CONTROL CONTROL
SA055617S-401CONTROL CONTROL
SA055618S-403CONTROL CONTROL
SA055619U-222CONTROL CONTROL
SA055620U-221CONTROL CONTROL
SA055621U-223CONTROL CONTROL
SA055622U-401CONTROL CONTROL
SA055623U-403CONTROL CONTROL
SA055624S-221CONTROL CONTROL
SA055625S-222CONTROL CONTROL
SA055626S-223CONTROL CONTROL
SA055627U-402CONTROL CONTROL
SA055628U-43INFECTED ADVANCED
SA055629U-162INFECTED ADVANCED
SA055630S-0041INFECTED ADVANCED
SA055631U-42INFECTED ADVANCED
SA055632S-0043INFECTED ADVANCED
SA055633U-41INFECTED ADVANCED
SA055634S-0042INFECTED ADVANCED
SA055635U-461INFECTED INFECTION-ONLY
SA055636U-463INFECTED INFECTION-ONLY
SA055637U-1122INFECTED INFECTION-ONLY
SA055638S-391INFECTED INFECTION-ONLY
SA055639U-462INFECTED INFECTION-ONLY
SA055640U-393INFECTED INFECTION-ONLY
SA055641S-462INFECTED INFECTION-ONLY
SA055642S-463INFECTED INFECTION-ONLY
SA055643S-461INFECTED INFECTION-ONLY
SA055644S-393INFECTED INFECTION-ONLY
SA055645U-392INFECTED INFECTION-ONLY
SA055646U-391INFECTED INFECTION-ONLY
SA055647S-392INFECTED INFECTION-ONLY
Showing results 1 to 32 of 32

Collection:

Collection ID:CO000967
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:blood and urine

Treatment:

Treatment ID:TR000987
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

Sample Preparation:

Sampleprep ID:SP000980
Sampleprep 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. MS acquisition was performed on the Q-Exactive hybrid quadrupole orbitrap mass spectrometer

Combined analysis:

Analysis ID AN001531
Analysis type MS
Chromatography type Reversed phase
Chromatography system Q-Exactive hybrid quadrupole orbitrap mass spectrometer
Column Hypersil Gold
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE
Units abundance of specific m/z (amu)

Chromatography:

Chromatography ID:CH001078
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.
Instrument Name:Q-Exactive hybrid quadrupole orbitrap mass spectrometer
Column Name:Hypersil Gold
Flow Rate:0.35ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS001411
Analysis ID:AN001531
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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