NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2397150 Query DataSets for GSM2397150
Status Public on Nov 01, 2017
Title 2S179_M_CAU_Y_4_8_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: 8
bmi: 30.4104
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 AB 0.025014 AB 5262.228027 13196.652344
SNP_A-1967418 BB 0.088439 BB 1540.600098 3085.842529
SNP_A-1969580 BB 0.003658 BB 3665.789062 14529.955078
SNP_A-4263484 BB 0.002746 BB 764.638550 2939.221436
SNP_A-1978185 AB 0.005389 AB 2453.652588 2647.625000
SNP_A-4264431 AB 0.004890 AB 2757.276611 1857.256470
SNP_A-1980898 BB 0.025392 BB 1278.172485 3303.905518
SNP_A-1983139 AA 0.002430 AA 7941.318359 1622.841187
SNP_A-4265735 AB 0.001993 AB 3841.103516 4362.673828
SNP_A-1995832 AB 0.006831 AB 5726.830078 4124.867188
SNP_A-1995893 AB 0.000720 AB 2905.476562 3052.188965
SNP_A-1997689 BB 0.004649 BB 1034.020752 4509.269043
SNP_A-1997709 AA 0.000540 AA 1735.942505 383.675385
SNP_A-1997896 AB 0.003247 AB 1566.841431 2605.501953
SNP_A-1997922 AB 0.009531 AB 727.236572 859.548523
SNP_A-2000230 AA 0.000742 AA 2995.982910 1277.112427
SNP_A-2000332 AB 0.001196 AB 3917.770996 3512.267334
SNP_A-2000337 AA 0.000403 AA 2113.676514 482.176971
SNP_A-2000342 AA 0.003379 AA 4343.043457 1281.262451
SNP_A-4268173 AA 0.004482 AA 3228.144531 642.663940

Total number of rows: 909622

Table truncated, full table size 46177 Kbytes.




Supplementary file Size Download File type/resource
GSM2397150_2S179.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM2397150_2S179.birdseed-v2.chp.gz 13.0 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