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Sample GSM549900 Query DataSets for GSM549900
Status Public on Jun 20, 2012
Title DGM-00447_gt
Sample type genomic
 
Source name Blood from healthy nonsmokers or healthy smokers
Organism Homo sapiens
Characteristics ethnicity: Afr
department of genetic medicine id: DGM-00447
smoking status: S
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions
Label biotin
Label protocol DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).
 
Hybridization protocol Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description n/a
Data processing The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method.
CHP files were created from CEL files after running BRLMM_p
 
Submission date Jun 03, 2010
Last update date Mar 05, 2013
Contact name Yael Strulovici-Barel
E-mail(s) yas2003@med.cornell.edu
Organization name Weill Cornell Medical College
Department Department of Genetic Medicine
Lab Crystal
Street address 1300 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL6804
Series (4)
GSE22047 Modulation of Cystatin A Expression in Human Airway Epithelium Related to Genotype, Smoking COPD and Lung Cancer
GSE23087 Genotype-Smoking Environment Interactions affecting eQTL in the Human Lung
GSE40364 eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
SNP_A-1780520 AB 0.000000 AB -0.100948 10.091581
SNP_A-1780618 BB 0.000000 BB -0.635832 10.207049
SNP_A-1780632 AA 0.000000 AA 0.851876 11.063318
SNP_A-1780654 AB 0.000000 AB -0.000444 11.683933
SNP_A-4192495 BB 0.000000 BB -0.831071 11.267960
SNP_A-4192498 AB 0.000000 AB 0.000812 11.340396
SNP_A-1780732 BB 0.000000 BB -0.601613 10.140602
SNP_A-1780848 AB 0.000000 AB 0.100426 10.490676
SNP_A-1780985 AB 0.000000 AB -0.139873 10.431591
SNP_A-1781076 AB 0.000000 AB 0.159811 10.745880
SNP_A-1781249 BB 0.000000 BB -0.768906 11.929561
SNP_A-1781276 AB 0.000000 AB -0.186628 10.658812
SNP_A-1781302 BB 0.000000 BB -0.808893 10.718810
SNP_A-1781510 AA 0.000035 AA 0.793783 11.080104
SNP_A-4192564 BB 0.000000 BB -0.479371 10.187863
SNP_A-1781614 AA 0.000000 AA 0.789420 10.295367
SNP_A-1781764 AB 0.000000 AB 0.053616 12.319979
SNP_A-1781829 AB 0.000000 AB -0.033231 11.422146
SNP_A-1782155 AB 0.000000 AB 0.017288 9.957371
SNP_A-1782305 AB 0.000000 AB 0.190038 10.777594

Total number of rows: 443816

Table truncated, full table size 20908 Kbytes.




Supplementary file Size Download File type/resource
GSM549900.CEL.gz 20.3 Mb (ftp)(http) CEL
GSM549900.CHP.gz 5.9 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table
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