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Sample GSM2397052 Query DataSets for GSM2397052
Status Public on Nov 01, 2017
Title 2S001_F_CAU_N_1_43_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: 43
bmi: 35.9109
diabetes: Y
hyperlipid: N
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 0.018105 AB 10503.548828 9399.085938
SNP_A-1967418 AB 0.018868 AB 4414.258301 4170.186035
SNP_A-1969580 BB 0.010713 BB 3897.911133 10023.711914
SNP_A-4263484 BB 0.012326 BB 2010.945557 4505.766113
SNP_A-1978185 NC 0.129029 AA 7902.445801 2407.087646
SNP_A-4264431 BB 0.001653 BB 1561.311157 4362.716309
SNP_A-1980898 BB 0.004556 BB 1019.123535 4084.007080
SNP_A-1983139 NC 0.139028 AA 6573.451660 3101.959961
SNP_A-4265735 BB 0.005129 BB 1981.560303 5423.796875
SNP_A-1995832 AB 0.013136 AB 4881.532715 4325.081055
SNP_A-1995893 AB 0.016044 AB 4036.181396 4908.577148
SNP_A-1997689 BB 0.012725 BB 1587.069946 4473.334961
SNP_A-1997709 AA 0.004652 AA 2308.125244 363.660706
SNP_A-1997896 AA 0.037226 AA 2095.460938 1412.069580
SNP_A-1997922 AB 0.023808 AB 1457.923340 1514.142212
SNP_A-2000230 AB 0.061769 AB 1950.281494 2807.617188
SNP_A-2000332 AB 0.007686 AB 2875.068604 2233.896484
SNP_A-2000337 AA 0.051874 AA 1167.030029 301.179321
SNP_A-2000342 AA 0.006977 AA 2502.372559 1058.991943
SNP_A-4268173 AA 0.002739 AA 1748.682617 345.350311

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM2397052_2S001.CEL.gz 30.8 Mb (ftp)(http) CEL
GSM2397052_2S001.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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