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Sample GSM2397107 Query DataSets for GSM2397107
Status Public on Nov 01, 2017
Title 2S101_F_CAU_N_1_110_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: N
cad class: 1
cxcl5 rank: 110
bmi: 30.335
diabetes: N
hyperlipid: N
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 0.002312 BB 845.016724 4844.738281
SNP_A-1967418 BB 0.000996 BB 530.914856 1992.085571
SNP_A-1969580 BB 0.007065 BB 3512.351318 9473.358398
SNP_A-4263484 AB 0.004250 AB 1854.309204 1055.870972
SNP_A-1978185 AA 0.003654 AA 1339.321167 309.513123
SNP_A-4264431 AA 0.001023 AA 2931.863770 487.996826
SNP_A-1980898 BB 0.026569 BB 357.852386 2346.064209
SNP_A-1983139 AA 0.002278 AA 5416.807617 1704.451660
SNP_A-4265735 NC 0.281098 AA 2721.828369 2752.280518
SNP_A-1995832 AB 0.004837 AB 3942.901367 3641.888672
SNP_A-1995893 NC 0.552229 AA 4249.867676 3419.810303
SNP_A-1997689 BB 0.002892 BB 699.091248 4181.335938
SNP_A-1997709 AA 0.041239 AA 3796.394043 317.786469
SNP_A-1997896 AB 0.018660 AB 2085.298096 2692.484863
SNP_A-1997922 AA 0.001669 AA 1074.704468 280.971375
SNP_A-2000230 NC 0.512145 AA 952.033875 1172.623779
SNP_A-2000332 AB 0.009774 AB 2117.342529 1864.226685
SNP_A-2000337 NC 0.411344 AB 811.845215 446.553070
SNP_A-2000342 AA 0.039393 AA 1695.347412 249.763412
SNP_A-4268173 AB 0.007729 AB 2324.089844 2031.360474

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.




Supplementary file Size Download File type/resource
GSM2397107_2S101.birdseed-v2.chp.gz 12.5 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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