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Sample GSM2397081 Query DataSets for GSM2397081
Status Public on Nov 01, 2017
Title 2S057_F_CAU_Y_2_89_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: 2
cxcl5 rank: 89
bmi: 23.7664
diabetes: N
hyperlipid: N
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 BB 0.008381 BB 1109.948486 11340.880859
SNP_A-1967418 AB 0.007556 AB 2960.894531 2364.104492
SNP_A-1969580 BB 0.009705 BB 5102.638184 13626.152344
SNP_A-4263484 AB 0.000537 AB 2607.037598 1904.543701
SNP_A-1978185 AA 0.004971 AA 3490.037109 439.679291
SNP_A-4264431 AA 0.008896 AA 4587.560059 622.553040
SNP_A-1980898 BB 0.004977 BB 541.247437 3691.241211
SNP_A-1983139 AA 0.011651 AA 6482.710449 1705.665161
SNP_A-4265735 AB 0.004172 AB 3455.338623 2828.368408
SNP_A-1995832 AB 0.008340 AB 4158.988770 3894.644775
SNP_A-1995893 AB 0.003865 AB 2954.938232 3133.937012
SNP_A-1997689 BB 0.008295 BB 949.062012 3330.749512
SNP_A-1997709 AA 0.008541 AA 1713.617188 422.925720
SNP_A-1997896 AA 0.003859 AA 2174.516602 648.845276
SNP_A-1997922 AB 0.005907 AB 580.089111 525.870483
SNP_A-2000230 AA 0.065565 AA 2224.172119 1283.474243
SNP_A-2000332 AA 0.014471 AA 4438.133301 944.144348
SNP_A-2000337 AA 0.005698 AA 1677.766602 238.917191
SNP_A-2000342 AA 0.004030 AA 2728.458984 962.844910
SNP_A-4268173 AB 0.009313 AB 2071.061035 1899.818604

Total number of rows: 909622

Table truncated, full table size 46159 Kbytes.




Supplementary file Size Download File type/resource
GSM2397081_2S057.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM2397081_2S057.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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