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Sample GSM2397118 Query DataSets for GSM2397118
Status Public on Nov 01, 2017
Title 2S119_M_CAU_N_1_136_genotype
Sample type genomic
 
Source name Whole blood, mononuclear cell extract
Organism Homo sapiens
Characteristics tissue: blood
cell type: mononuclear
gender: M
self_reported_race: CAU
ancestry: CAU
obstructive_cad: N
cad class: 1
cxcl5 rank: 136
bmi: 21.369
diabetes: N
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 0.003972 AA 10243.764648 1326.842651
SNP_A-1967418 AB 0.002298 AB 2587.204834 2243.750244
SNP_A-1969580 BB 0.005356 BB 5588.145020 16276.919922
SNP_A-4263484 BB 0.001271 BB 802.808655 3080.673584
SNP_A-1978185 AA 0.002077 AA 3499.746094 392.115509
SNP_A-4264431 AA 0.003045 AA 3884.064697 448.147186
SNP_A-1980898 BB 0.000539 BB 507.143494 3232.844482
SNP_A-1983139 AA 0.003188 AA 8015.889160 1665.919800
SNP_A-4265735 AA 0.000914 AA 5388.393555 816.267273
SNP_A-1995832 AB 0.001030 AB 4185.677734 3735.201904
SNP_A-1995893 AB 0.001639 AB 2481.934326 2510.943848
SNP_A-1997689 BB 0.001950 BB 700.947144 3202.641846
SNP_A-1997709 AA 0.001520 AA 2240.529785 348.933075
SNP_A-1997896 AA 0.002290 AA 1778.116943 519.388611
SNP_A-1997922 AB 0.001772 AB 811.661438 668.940125
SNP_A-2000230 AA 0.007429 AA 2967.126465 879.917175
SNP_A-2000332 AB 0.003469 AB 3275.834473 3288.958740
SNP_A-2000337 AA 0.003900 AA 2349.278809 329.232849
SNP_A-2000342 AA 0.005332 AA 3877.824707 819.075500
SNP_A-4268173 AA 0.004409 AA 3480.445557 654.704590

Total number of rows: 909622

Table truncated, full table size 46166 Kbytes.




Supplementary file Size Download File type/resource
GSM2397118_2S119.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM2397118_2S119.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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