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Sample GSM2397088 Query DataSets for GSM2397088
Status Public on Nov 01, 2017
Title 2S066_F_CAU_Y_4_56_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: 56
bmi: 23.642
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 NC 0.146055 BB 816.060913 6571.496582
SNP_A-1967418 AB 0.002010 AB 1296.446411 1234.023804
SNP_A-1969580 BB 0.006288 BB 2540.450684 9707.746094
SNP_A-4263484 BB 0.000697 BB 647.483521 2552.192871
SNP_A-1978185 AA 0.001261 AA 2206.244385 489.796783
SNP_A-4264431 AA 0.000693 AA 3394.399902 607.901733
SNP_A-1980898 NC 0.105406 BB 348.706635 2042.322510
SNP_A-1983139 AA 0.007434 AA 5166.196289 1192.804199
SNP_A-4265735 AA 0.004948 AA 3368.240723 719.153015
SNP_A-1995832 AB 0.003263 AB 3128.979248 3037.019287
SNP_A-1995893 AB 0.003027 AB 2716.582520 2838.827148
SNP_A-1997689 BB 0.001812 BB 751.342285 4213.265137
SNP_A-1997709 AA 0.004056 AA 2175.263428 320.741577
SNP_A-1997896 AB 0.004572 AB 1256.848389 2115.460205
SNP_A-1997922 AA 0.001842 AA 1077.330933 289.881226
SNP_A-2000230 AA 0.077330 AA 2317.636230 1373.397339
SNP_A-2000332 AA 0.002051 AA 3665.618652 975.145935
SNP_A-2000337 AA 0.001763 AA 1818.494141 425.966797
SNP_A-2000342 AA 0.008560 AA 2390.220947 771.124451
SNP_A-4268173 AA 0.012445 AA 3118.807617 429.005951

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM2397088_2S066.CEL.gz 30.7 Mb (ftp)(http) CEL
GSM2397088_2S066.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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