NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2397148 Query DataSets for GSM2397148
Status Public on Nov 01, 2017
Title 2S176_M_AA_N_1_97_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: AA
ancestry: AA
obstructive_cad: N
cad class: 1
cxcl5 rank: 97
bmi: 33.8628
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 0.000749 BB 1270.606079 9175.605469
SNP_A-1967418 BB 0.002367 BB 712.069458 4325.431152
SNP_A-1969580 BB 0.001045 BB 4891.590820 13677.142578
SNP_A-4263484 AB 0.015495 AB 4409.670410 4044.170166
SNP_A-1978185 AA 0.007466 AA 5438.634766 770.443115
SNP_A-4264431 AA 0.009141 AA 5394.001953 866.458252
SNP_A-1980898 BB 0.002688 BB 520.382019 3868.092285
SNP_A-1983139 AA 0.009539 AA 8806.602539 3008.529297
SNP_A-4265735 AA 0.001479 AA 5941.816406 1366.806885
SNP_A-1995832 BB 0.000477 BB 1338.789062 5642.827637
SNP_A-1995893 AB 0.008900 AB 2738.809814 3969.125732
SNP_A-1997689 BB 0.001373 BB 776.598206 3939.441406
SNP_A-1997709 AA 0.003664 AA 1525.824585 381.139679
SNP_A-1997896 AA 0.007255 AA 2768.641357 943.122253
SNP_A-1997922 BB 0.008326 BB 602.497131 1800.862671
SNP_A-2000230 AA 0.012724 AA 3758.185791 2067.879150
SNP_A-2000332 BB 0.002406 BB 1901.188965 5638.351074
SNP_A-2000337 AA 0.018136 AA 2331.597656 572.328247
SNP_A-2000342 AA 0.013525 AA 4240.237305 1496.028442
SNP_A-4268173 AB 0.006446 AB 2863.238525 2922.573242

Total number of rows: 909622

Table truncated, full table size 46176 Kbytes.




Supplementary file Size Download File type/resource
GSM2397148_2S176.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM2397148_2S176.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap