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Sample GSM2397141 Query DataSets for GSM2397141
Status Public on Nov 01, 2017
Title 2S160_M_CAU_Y_2_76_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: 76
bmi: 29.0312
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 0.014517 BB 825.543457 6900.081543
SNP_A-1967418 AB 0.010607 AB 3051.076904 2774.883789
SNP_A-1969580 BB 0.000350 BB 5694.699219 16611.703125
SNP_A-4263484 BB 0.003732 BB 500.965942 2456.132568
SNP_A-1978185 AA 0.000236 AA 3777.152832 484.863678
SNP_A-4264431 AA 0.003168 AA 5873.318848 647.713501
SNP_A-1980898 BB 0.001011 BB 672.338013 4349.050293
SNP_A-1983139 AA 0.005427 AA 9939.103516 1790.605713
SNP_A-4265735 AA 0.000517 AA 6835.377441 1174.410767
SNP_A-1995832 BB 0.008456 BB 1532.461914 7970.652832
SNP_A-1995893 BB 0.000478 BB 870.258118 4358.024414
SNP_A-1997689 BB 0.010246 BB 1020.334290 2519.263428
SNP_A-1997709 AA 0.007331 AA 967.967346 412.519318
SNP_A-1997896 BB 0.003232 BB 1118.683350 4465.613770
SNP_A-1997922 NC 0.495830 AA 958.057251 534.560059
SNP_A-2000230 AA 0.004083 AA 2670.961426 1427.330811
SNP_A-2000332 AB 0.006155 AB 4476.000977 4728.569824
SNP_A-2000337 AA 0.003083 AA 1598.150513 487.714294
SNP_A-2000342 AA 0.001703 AA 4022.879395 1187.366821
SNP_A-4268173 AA 0.015607 AA 7682.128418 1089.528320

Total number of rows: 909622

Table truncated, full table size 46182 Kbytes.




Supplementary file Size Download File type/resource
GSM2397141_2S160.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM2397141_2S160.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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