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Sample GSM2397077 Query DataSets for GSM2397077
Status Public on Nov 01, 2017
Title 2S051_M_CAU_N_0_109_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: N
cad class: 0
cxcl5 rank: 109
bmi: 27.6321
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 0.003109 BB 1088.235229 10255.191406
SNP_A-1967418 BB 0.005181 BB 597.534973 3162.343750
SNP_A-1969580 BB 0.004886 BB 2733.915527 9639.966797
SNP_A-4263484 BB 0.001353 BB 710.810242 2807.524170
SNP_A-1978185 AA 0.001952 AA 1886.747803 431.695435
SNP_A-4264431 AB 0.001944 AB 2203.414795 1515.785889
SNP_A-1980898 AB 0.003388 AB 1812.376953 1346.086426
SNP_A-1983139 AA 0.003082 AA 3596.482666 899.219971
SNP_A-4265735 AB 0.002262 AB 1576.791870 1856.494873
SNP_A-1995832 AB 0.000611 AB 2521.484131 2097.398438
SNP_A-1995893 AB 0.005140 AB 2508.176270 2456.297363
SNP_A-1997689 BB 0.004349 BB 831.396729 3509.690918
SNP_A-1997709 AA 0.009541 AA 1475.250732 328.360840
SNP_A-1997896 AA 0.002124 AA 1657.383179 520.373291
SNP_A-1997922 AB 0.003597 AB 699.609863 562.821045
SNP_A-2000230 AA 0.011890 AA 2730.300781 1224.889404
SNP_A-2000332 AA 0.002661 AA 3844.932617 1051.333984
SNP_A-2000337 AA 0.003025 AA 2099.282227 308.475037
SNP_A-2000342 AA 0.002905 AA 3412.912109 825.091858
SNP_A-4268173 BB 0.003225 BB 346.849640 1771.195190

Total number of rows: 909622

Table truncated, full table size 46152 Kbytes.




Supplementary file Size Download File type/resource
GSM2397077_2S051.CEL.gz 30.8 Mb (ftp)(http) CEL
GSM2397077_2S051.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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