Summary of Study ST000104

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 PR000096. The data can be accessed directly via it's Project DOI: 10.21228/M8NK5J This work is supported by NIH grant, U2C- DK119886.

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Study IDST000104
Study TitleFactors for Epigenetic Silencing of Lung Cancer Genes
Study TypeMetabolomic analysis of Plasma
Study SummaryTo test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNAÕs that directly or indirectly influence de novo methylation and chromatin remodeling.
Institute
University of North Carolina
DepartmentDiscovery Science Technology
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2014-09-29
Num Groups3
Total Subjects69
Raw Data AvailableYes
Raw Data File Type(s)fid
Uploaded File Size36 M
Analysis Type DetailNMR
Release Date2016-06-18
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8NK5J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000096
Project DOI:doi: 10.21228/M8NK5J
Project Title:Factors for Epigenetic Silencing of Lung Cancer Genes
Project Type:Metabolomics
Project Summary:To test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNA’s that directly or indirectly influence de novo methylation and chromatin remodeling.
Institute:Lovelace Respiratory Research Institute
Department:Lung Cancer Program
Last Name:Belinsky
First Name:Steven
Address:Lovelace Respiratory Research Institute, 2425 ridgecrest Dr, SE, Albuqurque, NM
Email:SBelinsk@lrri.org
Phone:505-348-9465
Funding Source:NCI

Subject:

Subject ID:SU000123
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:40-76
Weight Or Weight Range:Normal, Overweight, Obese
Gender:male , female
Human Smoking Status:former
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Gender bmi_cat drc_rank methylation_rank Pack Years
SA005677PPALL0002External_Pooled_Combined_QC - - - -
SA005678PPALL0001External_Pooled_Combined_QC - - - -
SA005679PPALL0003External_Pooled_Combined_QC - - - -
SA005680PLO_00002External_Pooled_Female_QC - - - -
SA005681PLO_00003External_Pooled_Female_QC - - - -
SA005682PLO_00001External_Pooled_Female_QC - - - -
SA005683PHI_00001External_Pooled_Male_QC - - - -
SA005684PHI_00003External_Pooled_Male_QC - - - -
SA005685PHI_00002External_Pooled_Male_QC - - - -
SA005686PLO_Met31Female Normal high low <70
SA005687PLO_Met44Female Normal high low <70
SA005688PLO_Met41Female Normal high low <70
SA005689PLO_Met32Female Normal high low <70
SA005690PHI_Met14Female Normal low high <70
SA005691PHI_Met07Female Normal low high <70
SA005692PHI_Met05Female Normal low high <70
SA005693PHI_Met02Female Normal low high <70
SA005694PHI_Met08Female Normal low high <70
SA005695PHI_Met03Female Normal low medium >= 70
SA005696PHI_Met29Female Normal not determined high <70
SA005697PLO_Met45Female Normal not determined low <70
SA005698PLO_Met46Female Normal not determined low <70
SA005699PLO_Met37Female Obese high low <70
SA005700PLO_Met35Female Obese high low <70
SA005701PHI_Met06Female Obese low high <70
SA005702PHI_Met13Female Obese low high <70
SA005703PHI_Met11Female Obese low high <70
SA005704PHI_Met16Female Obese not determined high <70
SA005705PHI_Met15Female Obese not determined high <70
SA005706PHI_Met17Female Obese not determined high <70
SA005707PHI_Met26Female Obese not determined high <70
SA005708PHI_Met28Female Obese not determined high <70
SA005709PHI_Met19Female Obese not determined high >= 70
SA005710PHI_Met27Female Obese not determined high >=70
SA005711PLO_Met50Female Obese not determined low <70
SA005712PLO_Met49Female Obese not determined low <70
SA005713PLO_Met48Female Obese not determined low <70
SA005714PLO_Met34Female Overwt high low <70
SA005715PLO_Met33Female Overwt high low <70
SA005716PHI_Met04Female Overwt low high <70
SA005717PHI_Met01Female Overwt low high <70
SA005718PHI_Met18Female Overwt not determined high <70
SA005719PHI_Met20Female Overwt not determined high <70
SA005720PLO_Met59Female Overwt not determined low <70
SA005721PLO_Met57Female Overwt not determined low <70
SA005722PLO_Met55Female Overwt not determined low <70
SA005723PLO_Met60Female Overwt not determined low <70
SA005724PLO_Met47Female Overwt not determined low <70
SA005725PHI_Met10Male Normal low high >= 70
SA005726PLO_Met40Male Normal low low <70
SA005727PLO_Met38Male Normal low medium <70
SA005728PHI_Met22Male Normal not determined high <70
SA005729PHI_Met25Male Normal not determined high >= 70
SA005730PLO_Met56Male Normal not determined low <70
SA005731PLO_Met39Male Obese high low <70
SA005732PHI_Met30Male Obese not determined high <70
SA005733PHI_Met23Male Obese not determined high <70
SA005734PHI_Met24Male Obese not determined high <70
SA005735PHI_Met21Male Obese not determined high <70
SA005736PLO_Met52Male Obese not determined low <70
SA005737PLO_Met51Male Obese not determined low >=70
SA005738PLO_Met43Male Overwt high medium <70
SA005739PHI_Met09Male Overwt low high <70
SA005740PHI_Met12Male Overwt low high <70
SA005741PLO_Met36Male Overwt low low <70
SA005742PLO_Met42Male Overwt low low >=70
SA005743PLO_Met53Male Overwt not determined low <70
SA005744PLO_Met54Male Overwt not determined low <70
Showing results 1 to 68 of 68

Collection:

Collection ID:CO000107
Collection Summary:-
Sample Type:plasma
Volumeoramount Collected:1000uL
Storage Conditions:-80
Additives:EDTA
Blood Serum Or Plasma:plasma

Treatment:

Treatment ID:TR000125
Treatment Summary:none

Sample Preparation:

Sampleprep ID:SP000120
Sampleprep Summary:Aliquots of plasma samples (630 µL) were transferred into labeled tubes for experimental samples. Pooled high methylatiion, low methylation and combined plasma samples were prepared to serve as external QC samples. For all samples 70 µL of 10 mM formate solution (chemical shift indicator) in 0.9% saline in D2O with 0.02% NaN3 was added to each tube and were vortexed for 30 sec then centrifuged at 12000 rcf for 5 min. A 600 µL aliquot of the supernatant was transferred into 5 mm NMR tubes, which were kept on ice until data acquisition.
Processing Storage Conditions:4°C
Extract Storage:-80C
Sample Resuspension:D2O Saline
Sample Spiking:formate

Analysis:

Analysis ID:AN000172
Laboratory Name:DHMRI
Analysis Type:NMR
Acquisition Date:41597
Software Version:TopSpin 2.1
Operator Name:Kevin Knagge, Wimal Pathmasiri
Randomization Order:Yes
Detector Type:NMR
Data Format:Bruker FID
Chromatography ID:CH000118
Num Factors:33

NMR:

NMR ID:NM000039
Analysis ID:AN000172
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:D20
Standard Concentration:1 mM
Spectrometer Frequency:700 MHz
NMR Probe:5mm Cryogenically Cooled ATMA
NMR Solvent:D20
NMR Tube Size:5mm
Shimming Method:Topshim (Gradient)
Pulse Sequence:cpmgpr1d
Water Suppression:yes
Pulse Width:11.2
Power Level:25.704 W
Receiver Gain:4.5
Offset Frequency:3300.70 Hz
Chemical Shift Ref Cpd:formate
Temperature:298 K
Number Of Scans:256
Dummy Scans:4
Acquisition Time:2.3243
Relaxation Delay:2s
Spectral Width:20.13 ppm
Num Data Points Acquired:65536
Real Data Points:65536
Line Broadening:0.5
Zero Filling:Yes
Apodization:Lorentzian
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:Formate
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