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Sample GSM2397099 Query DataSets for GSM2397099
Status Public on Nov 01, 2017
Title 2S087_M_CAU_Y_4_108_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: 4
cxcl5 rank: 108
bmi: 35.5796
diabetes: N
hyperlipid: Y
hypertension: N
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 0.007373 BB 1190.130615 11564.569336
SNP_A-1967418 BB 0.006567 BB 763.479370 4775.724121
SNP_A-1969580 BB 0.003675 BB 3627.498047 10375.485352
SNP_A-4263484 AB 0.003014 AB 2554.703369 1488.911987
SNP_A-1978185 AA 0.001623 AA 2776.139648 438.013977
SNP_A-4264431 AA 0.001293 AA 3836.223633 701.132141
SNP_A-1980898 AB 0.002933 AB 2084.583008 1791.113037
SNP_A-1983139 AA 0.008457 AA 7426.499512 2293.965576
SNP_A-4265735 NC 0.191151 AA 5674.144531 1050.664673
SNP_A-1995832 BB 0.005732 BB 1385.940796 5913.218262
SNP_A-1995893 BB 0.000679 BB 847.845642 3638.837646
SNP_A-1997689 BB 0.006359 BB 494.772736 3427.952393
SNP_A-1997709 AA 0.001234 AA 1648.389160 367.172852
SNP_A-1997896 AB 0.003009 AB 931.499023 1656.808472
SNP_A-1997922 AB 0.010036 AB 443.043274 348.790863
SNP_A-2000230 AA 0.060006 AA 2006.221802 1035.364502
SNP_A-2000332 AB 0.000637 AB 2784.201172 2723.792480
SNP_A-2000337 AB 0.008808 AB 1112.419556 752.068665
SNP_A-2000342 AA 0.027227 AA 2122.210449 349.405884
SNP_A-4268173 AA 0.004045 AA 2862.098389 495.923187

Total number of rows: 909622

Table truncated, full table size 46101 Kbytes.




Supplementary file Size Download File type/resource
GSM2397099_2S087.birdseed-v2.chp.gz 12.5 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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