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Sample GSM2397091 Query DataSets for GSM2397091
Status Public on Nov 01, 2017
Title 2S073_M_CAU_N_1_45_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: 45
bmi: 24.7052
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 0.012253 AB 8748.603516 9046.709961
SNP_A-1967418 BB 0.021222 BB 709.773315 5906.277344
SNP_A-1969580 BB 0.010223 BB 3873.137451 10008.635742
SNP_A-4263484 BB 0.002424 BB 356.452820 2123.557617
SNP_A-1978185 AA 0.000449 AA 2915.455566 542.653687
SNP_A-4264431 AA 0.003696 AA 4251.994629 714.299072
SNP_A-1980898 AB 0.004596 AB 2121.902100 1525.125000
SNP_A-1983139 AA 0.008431 AA 5542.236816 1334.934082
SNP_A-4265735 AB 0.001368 AB 2701.073730 2459.212402
SNP_A-1995832 AB 0.005038 AB 3799.759277 3174.429199
SNP_A-1995893 AB 0.002198 AB 2435.208740 2528.538330
SNP_A-1997689 BB 0.023540 BB 1051.154907 3126.218994
SNP_A-1997709 AA 0.010516 AA 1354.553589 258.382324
SNP_A-1997896 AA 0.002377 AA 1479.627808 551.234680
SNP_A-1997922 AB 0.024093 AB 418.818176 472.186584
SNP_A-2000230 AA 0.082058 AA 2145.500977 1287.170776
SNP_A-2000332 AA 0.003559 AA 3831.590088 953.724976
SNP_A-2000337 AA 0.014077 AA 1393.942261 312.410034
SNP_A-2000342 AA 0.013003 AA 2497.681885 624.596985
SNP_A-4268173 AA 0.003361 AA 2631.270996 440.863312

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM2397091_2S073.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM2397091_2S073.birdseed-v2.chp.gz 12.7 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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