NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2397106 Query DataSets for GSM2397106
Status Public on Nov 01, 2017
Title 2S100_F_CAU_Y_2_118_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: 2
cxcl5 rank: 118
bmi: 30.0132
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 BB 0.001382 BB 1255.437866 9894.225586
SNP_A-1967418 BB 0.001513 BB 706.182190 3876.870117
SNP_A-1969580 BB 0.007661 BB 3331.928467 11416.835938
SNP_A-4263484 AB 0.005636 AB 3739.923096 2888.600830
SNP_A-1978185 AA 0.009717 AA 5559.499023 852.356934
SNP_A-4264431 AA 0.005502 AA 3984.197266 508.381989
SNP_A-1980898 AB 0.009716 AB 3149.555908 2755.805664
SNP_A-1983139 AA 0.012953 AA 6846.368652 1867.123779
SNP_A-4265735 AA 0.017312 AA 5753.604980 1266.843262
SNP_A-1995832 BB 0.002101 BB 1166.531372 4800.128418
SNP_A-1995893 BB 0.007429 BB 982.199463 4699.788574
SNP_A-1997689 BB 0.001269 BB 1059.050903 4654.230957
SNP_A-1997709 AA 0.002820 AA 2038.560181 340.475586
SNP_A-1997896 AA 0.004717 AA 1851.876587 464.845459
SNP_A-1997922 AB 0.003033 AB 890.899414 966.373169
SNP_A-2000230 NC 0.460524 AB 2755.531982 1898.243408
SNP_A-2000332 AB 0.000916 AB 2570.530762 2597.506836
SNP_A-2000337 AA 0.004269 AA 2268.803223 437.430359
SNP_A-2000342 AA 0.000450 AA 3607.767090 951.901550
SNP_A-4268173 AA 0.005418 AA 2729.757324 414.362518

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM2397106_2S100.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM2397106_2S100.birdseed-v2.chp.gz 13.1 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