Summary of Study ST000614

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 PR000449. The data can be accessed directly via it's Project DOI: 10.21228/M8161N This work is supported by NIH grant, U2C- DK119886.

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Study IDST000614
Study TitleTobacco-specific carcinogens in Bladder Cancer
Study SummarySmoking induced methylation plays a critical role in the accumulation of methylated metabolites, DNA adducts damage and altered metabolism in BCa. These deregulated metabolites can be detected non-invasively and can be used as causal biomarkers that can predict the risk of developing BCa in smokers
Institute
Baylor College of Medicine
Last NamePutluri
First NameNagireddy
AddressOne Baylor Plaza
Emailputluri@bcm.edu
Phone7137983144
Submit Date2017-05-23
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Nagireddy Putluri Nagireddy Putluri
https://dx.doi.org/10.21228/M8161N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000449
Project DOI:doi: 10.21228/M8161N
Project Title:Tobacco-specific carcinogens induce hypermethylation, DNA adducts and DNA damage in Bladder Cancer
Project Summary:Smoking is a major risk factor for the development of Bladder cancer (BCa); however, the metabolic alterations and functional consequences associated with cigarette smoke carcinogens in BCa remain poorly defined. We assessed the metabolic profile in BCa and identified the key alterations in metabolism associated with smoking.
Institute:Baylor College of Medicine
Last Name:Putluri
First Name:Nagireddy
Address:One Baylor Plaza, Houston, TX, 77030, USA
Email:putluri@bcm.edu
Phone:713-798-3139

Subject:

Subject ID:SU000637
Subject Type:Bladder Cancer Tissues
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: Bladder Cancer Tissues; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Diagonsis Smoking Status
SA03393721813-NBenign Smoker
SA03393822186-1NBenign Smoker
SA03393920500-1 NBenign Smoker
SA03394019071-1 NBenign Smoker
SA03394118132-1NBenign Smoker
SA03394222201-3 NBenign Smoker
SA03394319627-1 NBenign Smoker
SA03394420636-1 NBenign Smoker
SA03394522018-1 NBenign Smoker
SA03394622233-1NBenign Smoker
SA03394721981-NBenign Smoker
SA03394820957-1 NBenign Smoker
SA03394913742-NBenign Smoker
SA03395019229-1NBenign Smoker
SA03395117F35E1FCancer Current Smoker
SA0339521afbc5b2Cancer Current Smoker
SA03395304755f1ccCancer Current Smoker
SA0339542192252cCancer Current Smoker
SA0339559B7DA93ACancer Current Smoker
SA03395622018Cancer Current Smoker
SA0339579AB7EADCCancer Current Smoker
SA0339585b47e65aCancer Current Smoker
SA0339595A929F9ECancer Current Smoker
SA033960H14335-13Cancer Current Smoker
SA03396113742Cancer Current Smoker
SA033962H16027-13Cancer Current Smoker
SA033963H13329-13Cancer Current Smoker
SA03396414021Cancer Current Smoker
SA03396516867Cancer Current Smoker
SA03396620957Cancer Current Smoker
SA03396719229Cancer Current Smoker
SA03396821981Cancer Current Smoker
SA033969H17407-14Cancer Current Smoker
SA033970H4545-14Cancer Current Smoker
SA033971H4407-14Cancer Current Smoker
SA033972H335-14Cancer Current Smoker
SA033973H6181-14Cancer Current Smoker
SA033974H6828-14Cancer Current Smoker
SA033975W768-13Cancer Current Smoker
SA033976W610-14Cancer Current Smoker
SA033977H13928Cancer Current Smoker
SA033978H2693-14Cancer Current Smoker
SA033979H8541-14Cancer Current Smoker
SA033980H20232-14Cancer Current Smoker
SA033981H21956-14Cancer Current Smoker
SA033982H20475-13Cancer Current Smoker
SA033983H17745-14Cancer Current Smoker
SA033984H21617-13Cancer Current Smoker
SA033985H21013-14Cancer Current Smoker
SA033986H20941-13Cancer Current Smoker
SA033987dac57f3dCancer Former Smoker
SA033988H00545-15Cancer Former Smoker
SA033989ddae2ceeCancer Former Smoker
SA0339904b24c7f3Cancer Former Smoker
SA033991H19025-13Cancer Former Smoker
SA03399231842d51Cancer Former Smoker
SA0339936394FAA2Cancer Former Smoker
SA033994H8220-14(H10472-14)Cancer Former Smoker
SA033995W114-14Cancer Former Smoker
SA033996276330f9Cancer Former Smoker
SA033997W00853-14Cancer Former Smoker
SA033998H6655-14(H5347-14)Cancer Former Smoker
SA033999H21551-14Cancer Former Smoker
SA034000H25045-13Cancer Former Smoker
SA034001H2153-14Cancer Former Smoker
SA034002a98f2fbeCancer Former Smoker
SA03400318132Cancer Former Smoker
SA03400416763Cancer Former Smoker
SA03400518890Cancer Former Smoker
SA03400619071Cancer Former Smoker
SA03400719627Cancer Former Smoker
SA03400816368Cancer Former Smoker
SA03400916276Cancer Former Smoker
SA034010H16912-13Cancer Former Smoker
SA034011200945e 4Cancer Former Smoker
SA034012H17983-13Cancer Former Smoker
SA034013H18484-14Cancer Former Smoker
SA0340144856Cancer Former Smoker
SA03401519801Cancer Former Smoker
SA0340168230Cancer Former Smoker
SA0340171b44fdcdCancer Former Smoker
SA0340180a15bd3cCancer Former Smoker
SA0340190d33871dCancer Former Smoker
SA0340200e54addbCancer Former Smoker
SA03402119846Cancer Former Smoker
SA03402222233Cancer Former Smoker
SA03402307d3d7e4Cancer Former Smoker
SA03402420636Cancer Former Smoker
SA03402520500Cancer Former Smoker
SA03402622186Cancer Former Smoker
SA03402721813Cancer Former Smoker
SA03402822201Cancer Former Smoker
SA034029H20182-13Cancer Non-Smoker
SA034030H20870-13Cancer Non-Smoker
SA034031H2059-14Cancer Non-Smoker
SA034032H20909-13Cancer Non-Smoker
SA034033H23671-13Cancer Non-Smoker
SA034034H25638-14Cancer Non-Smoker
SA034035H1947-14Cancer Non-Smoker
SA034036H22582-13Cancer Non-Smoker
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Collection:

Collection ID:CO000631
Collection Summary:Witten-Herdecke University;The University of Texas Southwestern Medical Center; Baylor College of Medicin
Sample Type:Bladder tissue

Treatment:

Treatment ID:TR000651
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP000644
Sampleprep Summary:All the tissues and urine samples used for this study were stored in -140oC. 50 mg of tissue was used for the extraction. For cell lines, 3 x106 cell pellets were thawed at 4 °C and subjected to three freeze-thaw cycles, freezing in liquid nitrogen and thawing on ice, to rupture the cell membranes. The extraction step start with 750 µL ice-cold methanol:water (4:1) containing 20 µL spiked internal standards was added to each cell pellet or tissue sample. Ice-cold chloroform and water was added in a 3:1 ratio for a final proportion of 1:4:3:1 water:methanol:chloroform:water. The organic (methanol and chloroform) and aqueous layers dried and re suspended with 50:50 methonal: water. The extract was deproteinized using a 3-kDa molecular filter (Amicon Ultracel-3K Membrane; Millipore Corporation, Billerica, MA) and the filtrate was dried under vacuum (Genevac EZ-2plus; Gardiner, Stone Ridge, NY). Prior to mass spectrometry, the dried extracts were resuspended in identical volumes of injection solvent composed of 1:1 water:methanol and subjected to liquid chromatography-mass spectrometry. 50 ul of urine was used for sample preparation. Internal standard was spiked into raw sample. Then it was processed through Amicon 3k filter. After that, 50 ul of urine sample was diluted with 450 solvent ( methanol water =50:50 v/v) and subjected to LC/MS analysis. The injection volume was 10 ul.

Combined analysis:

Analysis ID AN000939 AN000940 AN000941 AN000942 AN000943
Analysis type MS MS MS MS MS
Chromatography type HILIC HILIC HILIC HILIC HILIC
Chromatography system Unspecified Unspecified Unspecified Unspecified Unspecified
Column Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Phenomenex Luna NH2 (150 x 2.1mm,3um)
MS Type ESI ESI ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ
Ion Mode POSITIVE NEGATIVE POSITIVE POSITIVE POSITIVE
Units Peak intensity Peak intensity Peak intensity Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH000670
Instrument Name:Unspecified
Column Name:Waters XBridge Amide (100 x 4.6mm,3.5um)
Chromatography Type:HILIC
  
Chromatography ID:CH000671
Instrument Name:Unspecified
Column Name:Phenomenex Luna NH2 (150 x 2.1mm,3um)
Chromatography Type:HILIC

MS:

MS ID:MS000835
Analysis ID:AN000939
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000836
Analysis ID:AN000940
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS000837
Analysis ID:AN000941
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000838
Analysis ID:AN000942
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000839
Analysis ID:AN000943
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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