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