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Sample GSM2397067 Query DataSets for GSM2397067
Status Public on Nov 01, 2017
Title 2S037_F_CAU_Y_4_46_genotype
Sample type genomic
 
Source name Whole blood, mononuclear cell extract
Organism Homo sapiens
Characteristics tissue: blood
cell type: mononuclear
gender: F
self_reported_race: CAU
ancestry: CAU
obstructive_cad: Y
cad class: 4
cxcl5 rank: 46
bmi: 28.474
diabetes: Y
hyperlipid: Y
hypertension: Y
Treatment protocol none
Growth protocol none
Extracted molecule genomic DNA
Extraction protocol Blood was drawn early in the day from fasted subjects to minimize signals associated with nutritional and diurnal cycle and processed within fifteen minutes. Plasma samples were obtained and RNA and DNA recovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).
Label biotin
Label protocol DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).
 
Hybridization protocol DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).
Scan protocol DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).
Data processing CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings.
CHP files were imported into Partek Genomics Suite v6.6. Genotype Call (SNP call): AA, AB, BB, or NC (No Call).
 
Submission date Nov 18, 2016
Last update date Nov 01, 2017
Contact name Jonathan C Schisler
E-mail(s) schisler@unc.edu
Phone 919-843-8708
Organization name The University of North Carolina at Chapel Hill
Department McAllister Heart Institute
Lab Schisler Lab
Street address MBRB, Rm 2340C
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7126
Country USA
 
Platform ID GPL6801
Series (2)
GSE90073 Genotyping data from Phase 2 of the SAMARA study (Supporting a Multi-disciplinary Approach to Researching Atherosclerosis)
GSE90076 Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease Progression in the Elderly

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.001120 AA 9858.820312 2574.505859
SNP_A-1967418 AB 0.002861 AB 2079.705811 1911.946045
SNP_A-1969580 BB 0.005531 BB 2500.176514 9415.332031
SNP_A-4263484 BB 0.011830 BB 701.088867 3621.768799
SNP_A-1978185 AA 0.006540 AA 4347.201172 581.174927
SNP_A-4264431 AA 0.001215 AA 2624.743652 364.058777
SNP_A-1980898 NC 0.298466 BB 287.998840 1848.342529
SNP_A-1983139 AA 0.003534 AA 4420.897949 1120.166748
SNP_A-4265735 AA 0.021004 AA 2503.888428 909.497192
SNP_A-1995832 NC 0.149120 BB 1370.682251 3349.312500
SNP_A-1995893 BB 0.003698 BB 1177.233521 3729.112549
SNP_A-1997689 BB 0.003726 BB 600.994629 3848.276855
SNP_A-1997709 AA 0.032988 AA 1053.804077 248.783951
SNP_A-1997896 AB 0.020032 AB 789.470703 1948.029419
SNP_A-1997922 AA 0.002748 AA 1047.467163 295.685181
SNP_A-2000230 NC 0.104355 AA 2556.311279 1538.826782
SNP_A-2000332 NC 0.434168 AB 3499.746338 2266.204590
SNP_A-2000337 AA 0.000858 AA 1920.193970 351.857941
SNP_A-2000342 AA 0.002594 AA 4154.206055 992.752197
SNP_A-4268173 AA 0.002934 AA 2532.669922 413.461670

Total number of rows: 909622

Table truncated, full table size 46149 Kbytes.




Supplementary file Size Download File type/resource
GSM2397067_2S037.CEL.gz 32.8 Mb (ftp)(http) CEL
GSM2397067_2S037.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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