Summary of Study ST001923

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 PR001214. The data can be accessed directly via it's Project DOI: 10.21228/M8SH7V 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 IDST001923
Study TitleUrine-Based Metabolomics and Machine Learning Reveals Metabolites Associated with Renal Cell Carcinoma Progression
Study SummaryEvery year, hundreds of thousands of cases of renal carcinoma (RCC) are reported worldwide. Accurate staging of the disease is important for treatment and prognosis purposes; however, contemporary methods such as computerized tomography (CT) and biopsies are expensive and prone to sampling errors, respectively. As such, a non-invasive diagnostic assay for staging would be beneficial. This study aims to investigate urine metabolites as potential biomarkers to stage RCC. In the study, we identified a panel of such urine metabolites with machine learning techniques.
Institute
University of Georgia
DepartmentDepartment of Biochemistry and Molecular Biology
LaboratoryEdison Lab
Last NameBifarin
First NameOlatomiwa
Address315 Riverbend Rd, Athens, GA 30602
Emailolatomiwa.bifarin25@uga.edu
Phone757-405-4379
Submit Date2021-08-16
Num GroupsTwo
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-10-18
Release Version1
Olatomiwa Bifarin Olatomiwa Bifarin
https://dx.doi.org/10.21228/M8SH7V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001214
Project DOI:doi: 10.21228/M8SH7V
Project Title:Urine-Based Metabolomics and Machine Learning Reveals Metabolites Associated with Renal Cell Carcinoma Progression
Project Type:multi-platform urine-based metabolomics
Project Summary:Every year, hundreds of thousands of cases of renal carcinoma (RCC) are reported worldwide. Accurate staging of the disease is important for treatment and prognosis purposes; however, contemporary methods such as computerized tomography (CT) and biopsies are expensive and prone to sampling errors, respectively. As such, a non-invasive diagnostic assay for staging would be beneficial. This study aims to investigate urine metabolites as potential biomarkers to stage RCC. In the study, we identified a panel of such urine metabolites with machine learning techniques.
Institute:University of Georgia
Department:Biochemistry and Molecular Biology
Laboratory:Fernandez Lab/ Edison Lab
Last Name:Bifarin
First Name:Olatomiwa
Address:315 Riverbend Rd, Athens, GA 30602
Email:olatomiwa.bifarin25@uga.edu
Phone:(706) 542-4401 Lab: 1045

Subject:

Subject ID:SU002001
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Factor
SA177936C036Early
SA177937C037Early
SA177938C039Early
SA177939C058Early
SA177940C102Early
SA177941C083Early
SA177942C095Early
SA177943C061Early
SA177944C084Early
SA177945C040Early
SA177946C057Early
SA177947C070Early
SA177948C049Early
SA177949C001Early
SA177950C053Early
SA177951C047Early
SA177952C046Early
SA177953C027Early
SA177954C054Early
SA177955C096Early
SA177956C101Early
SA177957C063Early
SA177958C009Early
SA177959C089Early
SA177960C012Early
SA177961C013Early
SA177962C081Early
SA177963C082Early
SA177964C088Early
SA177965C093Early
SA177966C092Early
SA177967C087Early
SA177968C091Early
SA177969C022Early
SA177970C024Early
SA177971C077Early
SA177972C062Early
SA177973C020Early
SA177974C016Early
SA177975C018Early
SA177976C085Early
SA177977C064Late
SA177978C073Late
SA177979C072Late
SA177980C078Late
SA177981C086Late
SA177982C099Late
SA177983C097Late
SA177984C066Late
SA177985C050Late
SA177986C026Late
SA177987C060Late
SA177988C030Late
SA177989C031Late
SA177990C025Late
SA177991C021Late
SA177992C011Late
SA177993C014Late
SA177994C015Late
SA177995C019Late
SA177996C033Late
SA177997C028Late
SA177998C048Late
SA177999C051Late
SA178000C059Late
SA178001C045Late
SA178002C044Late
SA178003C043Late
SA178004C041Late
SA178005C038Late
SA178006C005Unknown
SA178007C006Unknown
SA178008C004Unknown
SA178009C007Unknown
SA178010C002Unknown
SA178011C003Unknown
SA178012C079Unknown
SA178013C074Unknown
SA178014C076Unknown
SA178015C034Unknown
SA178016C065Unknown
SA178017C052Unknown
Showing results 1 to 82 of 82

Collection:

Collection ID:CO001994
Collection Summary:Urine samples were collected at the Emory University Hospital
Collection Protocol Filename:2_Collection_protocol_RCC_AUG2021.docx
Sample Type:Urine

Treatment:

Treatment ID:TR002013
Treatment Summary:There were no treatment in the study, urine samples of healthy subjects and renal cell carcinoma patients were collected.

Sample Preparation:

Sampleprep ID:SP002007
Sampleprep Summary:Urine’s samples were prepared for both NMR and MS experiments
Sampleprep Protocol Filename:3_Sample preparation protocol_RCC_AUG2021.docx
Processing Storage Conditions:-80℃

Combined analysis:

Analysis ID AN003125 AN003126
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Q Exactive HF Q Exactive HF
Column Waters ACQUITY UPLC BEH HILIC (75 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH HILIC (75 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units AU AU

Chromatography:

Chromatography ID:CH002310
Instrument Name:Q Exactive HF
Column Name:Waters ACQUITY UPLC BEH HILIC (75 x 2.1mm,1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS002906
Analysis ID:AN003125
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:--
Ion Mode:POSITIVE
  
MS ID:MS002907
Analysis ID:AN003126
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:--
Ion Mode:NEGATIVE
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