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Sample GSM2397057 Query DataSets for GSM2397057
Status Public on Nov 01, 2017
Title 2S007_F_CAU_Y_4_39_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: Y
cad class: 4
cxcl5 rank: 39
bmi: 28.8718
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 BB 0.005810 BB 1059.031860 8008.424805
SNP_A-1967418 NC 0.115290 BB 512.713745 2407.126953
SNP_A-1969580 BB 0.004916 BB 2613.169434 7923.225586
SNP_A-4263484 AB 0.001583 AB 2895.677490 2314.641602
SNP_A-1978185 AA 0.004441 AA 3301.728760 842.347778
SNP_A-4264431 AB 0.000660 AB 1787.538818 1533.052734
SNP_A-1980898 AB 0.003908 AB 2027.482544 1510.771851
SNP_A-1983139 AA 0.003209 AA 5035.380859 1498.132812
SNP_A-4265735 AA 0.004401 AA 3442.737793 794.159912
SNP_A-1995832 AB 0.004618 AB 3718.833496 3076.391113
SNP_A-1995893 AB 0.007295 AB 3493.875488 3845.861084
SNP_A-1997689 BB 0.013236 BB 1136.121582 6049.376465
SNP_A-1997709 AA 0.007718 AA 2628.407715 453.094696
SNP_A-1997896 AB 0.019773 AB 1903.506470 2666.349854
SNP_A-1997922 AA 0.069669 AA 2140.766846 379.479462
SNP_A-2000230 NC 0.635380 AB 2255.621338 1704.502930
SNP_A-2000332 BB 0.006135 BB 1779.721191 3616.528564
SNP_A-2000337 AA 0.003046 AA 1740.635254 430.190125
SNP_A-2000342 AA 0.003383 AA 2961.320068 1051.379883
SNP_A-4268173 AA 0.002160 AA 2377.597656 554.064758

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM2397057_2S007.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM2397057_2S007.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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