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Sample GSM2397140 Query DataSets for GSM2397140
Status Public on Nov 01, 2017
Title 2S154_F_CAU_Y_4_9_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: 4
cxcl5 rank: 9
bmi: 38.4488
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 0.003826 BB 1163.788696 7337.700195
SNP_A-1967418 BB 0.002996 BB 548.686768 3990.364014
SNP_A-1969580 BB 0.004482 BB 6029.211426 15036.723633
SNP_A-4263484 BB 0.015053 BB 1068.407593 4825.554688
SNP_A-1978185 AA 0.005428 AA 4308.451660 424.412323
SNP_A-4264431 AA 0.008763 AA 6257.926758 762.531433
SNP_A-1980898 BB 0.007720 BB 776.442261 5257.148926
SNP_A-1983139 AA 0.007231 AA 9196.052734 2965.093506
SNP_A-4265735 AA 0.000481 AA 5516.540527 943.410706
SNP_A-1995832 AB 0.005610 AB 5044.445312 4820.586914
SNP_A-1995893 AB 0.024458 AB 4452.056152 4277.180176
SNP_A-1997689 BB 0.002508 BB 677.883301 3551.935059
SNP_A-1997709 AA 0.002151 AA 2410.706543 381.709747
SNP_A-1997896 AA 0.010970 AA 3049.845947 579.925232
SNP_A-1997922 AB 0.008706 AB 1044.360352 964.373596
SNP_A-2000230 AA 0.007509 AA 3233.391357 1788.839966
SNP_A-2000332 AB 0.008097 AB 4552.681152 4430.393555
SNP_A-2000337 AA 0.008864 AA 2362.328857 280.462982
SNP_A-2000342 AA 0.000566 AA 4030.229492 1046.510376
SNP_A-4268173 AA 0.031646 AA 6451.342285 1171.155640

Total number of rows: 909622

Table truncated, full table size 46169 Kbytes.




Supplementary file Size Download File type/resource
GSM2397140_2S154.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM2397140_2S154.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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