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Sample GSM2397146 Query DataSets for GSM2397146
Status Public on Nov 01, 2017
Title 2S171_M_CAU_Y_2_35_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: Y
cad class: 2
cxcl5 rank: 35
bmi: 39.8367
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 BB 0.000688 BB 1208.424683 9234.370117
SNP_A-1967418 BB 0.001301 BB 711.788513 3558.625000
SNP_A-1969580 BB 0.006284 BB 6401.466797 16625.990234
SNP_A-4263484 AA 0.018776 AA 4084.553467 348.172791
SNP_A-1978185 AA 0.000297 AA 3534.791016 502.463593
SNP_A-4264431 AB 0.004651 AB 3833.731201 2904.327881
SNP_A-1980898 AB 0.009040 AB 3163.434082 2964.736328
SNP_A-1983139 AA 0.001361 AA 8505.769531 2169.246338
SNP_A-4265735 AA 0.002290 AA 5573.977539 1322.733276
SNP_A-1995832 AA 0.010788 AA 6670.136230 861.659363
SNP_A-1995893 AA 0.006187 AA 5871.956055 1981.604248
SNP_A-1997689 BB 0.001391 BB 723.039856 3251.241699
SNP_A-1997709 AA 0.000195 AA 1924.880371 352.431976
SNP_A-1997896 AA 0.004182 AA 2671.403809 608.613464
SNP_A-1997922 AA 0.015080 AA 890.097351 273.685211
SNP_A-2000230 AA 0.007012 AA 2292.167725 1269.619141
SNP_A-2000332 AA 0.000499 AA 5704.393066 1045.835327
SNP_A-2000337 AA 0.008057 AA 1634.649048 347.028717
SNP_A-2000342 AA 0.003172 AA 3560.320557 994.046387
SNP_A-4268173 AA 0.018955 AA 5312.897461 729.837097

Total number of rows: 909622

Table truncated, full table size 46172 Kbytes.




Supplementary file Size Download File type/resource
GSM2397146_2S171.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM2397146_2S171.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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