NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2397126 Query DataSets for GSM2397126
Status Public on Nov 01, 2017
Title 2S137_M_CAU_Y_4_14_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: 14
bmi: 30.6021
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 AB 0.001088 AB 6025.415527 7112.255859
SNP_A-1967418 BB 0.001112 BB 647.231995 3972.841309
SNP_A-1969580 BB 0.004972 BB 5586.136230 19772.417969
SNP_A-4263484 AB 0.002220 AB 4279.789551 3102.911377
SNP_A-1978185 AA 0.004935 AA 5665.425781 735.427612
SNP_A-4264431 AA 0.002059 AA 5455.332520 936.192139
SNP_A-1980898 AB 0.006789 AB 4366.973633 3668.773438
SNP_A-1983139 AA 0.001896 AA 10679.593750 2918.148682
SNP_A-4265735 AB 0.002252 AB 5093.123047 5455.661621
SNP_A-1995832 AA 0.008285 AA 8604.943359 1783.158691
SNP_A-1995893 AA 0.007223 AA 6626.021973 2707.948975
SNP_A-1997689 BB 0.008710 BB 1074.979614 5109.679688
SNP_A-1997709 AA 0.011729 AA 3520.338623 552.134888
SNP_A-1997896 AA 0.004089 AA 3133.244873 1017.185791
SNP_A-1997922 AA 0.007930 AA 1766.471802 639.640076
SNP_A-2000230 AA 0.013127 AA 3207.999268 1933.948364
SNP_A-2000332 AB 0.001875 AB 4088.708496 3626.472900
SNP_A-2000337 AA 0.009334 AA 2787.706543 668.264893
SNP_A-2000342 AA 0.025767 AA 4157.966309 1698.401123
SNP_A-4268173 AA 0.001749 AA 4832.666016 888.311096

Total number of rows: 909622

Table truncated, full table size 46165 Kbytes.




Supplementary file Size Download File type/resource
GSM2397126_2S137.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM2397126_2S137.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