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Sample GSM2397138 Query DataSets for GSM2397138
Status Public on Nov 01, 2017
Title 2S152_F_CAU_Y_2_10_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: 10
bmi: 25.749
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 0.000850 BB 1012.805481 8192.814453
SNP_A-1967418 BB 0.002272 BB 759.306763 4423.073730
SNP_A-1969580 BB 0.007558 BB 6542.919434 17202.275391
SNP_A-4263484 AB 0.005691 AB 4012.194092 2619.595215
SNP_A-1978185 AA 0.003272 AA 4381.478027 516.875305
SNP_A-4264431 AA 0.012172 AA 5999.539551 603.550110
SNP_A-1980898 BB 0.007516 BB 598.649536 4876.498535
SNP_A-1983139 AA 0.005671 AA 9263.642578 2860.840088
SNP_A-4265735 AA 0.001576 AA 6328.172852 1334.513550
SNP_A-1995832 AB 0.001715 AB 4388.946777 3982.989258
SNP_A-1995893 AB 0.004760 AB 3313.244385 3537.150635
SNP_A-1997689 BB 0.002943 BB 787.893860 3049.560791
SNP_A-1997709 AA 0.004277 AA 2354.078857 435.037048
SNP_A-1997896 AA 0.012916 AA 2837.144531 457.368988
SNP_A-1997922 AB 0.001116 AB 717.848450 706.078857
SNP_A-2000230 AA 0.001007 AA 3146.809570 1255.801025
SNP_A-2000332 AA 0.014366 AA 6837.712891 827.576904
SNP_A-2000337 AA 0.001781 AA 2579.669678 409.121307
SNP_A-2000342 AA 0.006908 AA 4873.028320 1013.527405
SNP_A-4268173 AA 0.025590 AA 5984.742188 981.575623

Total number of rows: 909622

Table truncated, full table size 46175 Kbytes.




Supplementary file Size Download File type/resource
GSM2397138_2S152.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM2397138_2S152.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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