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Sample GSM2397151 Query DataSets for GSM2397151
Status Public on Nov 01, 2017
Title 2S184_M_AA_Y_3_18_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: AA
obstructive_cad: Y
cad class: 3
cxcl5 rank: 18
bmi: 22.5534
diabetes: N
hyperlipid: N
hypertension: N
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 0.003194 AB 7585.499512 7943.299316
SNP_A-1967418 BB 0.000426 BB 751.470215 3963.013916
SNP_A-1969580 BB 0.003880 BB 3514.156250 10374.815430
SNP_A-4263484 AB 0.004487 AB 3720.075684 3059.308594
SNP_A-1978185 AB 0.003455 AB 3088.065674 4587.619629
SNP_A-4264431 AB 0.001231 AB 3309.428467 2560.954834
SNP_A-1980898 AB 0.004113 AB 2270.421631 2155.691895
SNP_A-1983139 AA 0.002453 AA 7037.782715 1445.245117
SNP_A-4265735 AB 0.000948 AB 3597.201172 3729.260986
SNP_A-1995832 BB 0.011295 BB 971.410828 3902.687012
SNP_A-1995893 BB 0.013297 BB 438.364471 2361.742188
SNP_A-1997689 BB 0.002389 BB 678.608948 3477.705811
SNP_A-1997709 AA 0.007417 AA 794.351135 244.676010
SNP_A-1997896 AB 0.009504 AB 2089.916504 2507.031250
SNP_A-1997922 AB 0.007628 AB 922.911743 1041.983154
SNP_A-2000230 AA 0.002835 AA 3746.745850 1583.668457
SNP_A-2000332 BB 0.001567 BB 1495.272217 5459.118652
SNP_A-2000337 AA 0.009292 AA 3129.946045 401.661957
SNP_A-2000342 AA 0.016975 AA 5830.279297 1412.138672
SNP_A-4268173 AA 0.003815 AA 3909.848389 445.805695

Total number of rows: 909622

Table truncated, full table size 46176 Kbytes.




Supplementary file Size Download File type/resource
GSM2397151_2S184.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM2397151_2S184.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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