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Sample GSM2397079 Query DataSets for GSM2397079
Status Public on Nov 01, 2017
Title 2S054_F_CAU_N_1_33_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: N
cad class: 1
cxcl5 rank: 33
bmi: 8.0428
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 AB 0.001517 AB 4071.669189 5317.728027
SNP_A-1967418 AB 0.025706 AB 334.252533 1605.235107
SNP_A-1969580 BB 0.005686 BB 3522.260498 9783.336914
SNP_A-4263484 BB 0.000810 BB 622.627441 2493.596436
SNP_A-1978185 AA 0.001451 AA 2193.711914 413.500519
SNP_A-4264431 AB 0.001285 AB 2296.298340 1765.235962
SNP_A-1980898 BB 0.004894 BB 329.790497 2493.894287
SNP_A-1983139 AA 0.003475 AA 5291.633789 1637.636841
SNP_A-4265735 AA 0.006465 AA 4103.248047 925.579163
SNP_A-1995832 AB 0.003191 AB 3385.487061 2780.049561
SNP_A-1995893 AB 0.006221 AB 3355.770996 3629.994385
SNP_A-1997689 BB 0.001418 BB 937.875793 4651.490723
SNP_A-1997709 AA 0.011089 AA 2816.583496 427.559113
SNP_A-1997896 AB 0.009948 AB 1672.355835 2416.885742
SNP_A-1997922 AA 0.005995 AA 1257.846436 176.348221
SNP_A-2000230 AA 0.098708 AA 1756.199341 1047.390381
SNP_A-2000332 AB 0.002862 AB 2350.203857 2718.638428
SNP_A-2000337 AA 0.007142 AA 1525.160156 338.385742
SNP_A-2000342 AA 0.013785 AA 2329.475098 634.990601
SNP_A-4268173 AA 0.011421 AA 3240.273438 511.078857

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM2397079_2S054.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM2397079_2S054.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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