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Sample GSM337749 Query DataSets for GSM337749
Status Public on Dec 10, 2008
Title 6_Affymetrix
Sample type genomic
Source name Blood
Organism Homo sapiens
Characteristics Gender: Female, Tumor content: 69%
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions.
Label Total genomic DNA was digested with a restriction enzyme (Nsp1), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer
Label protocol After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase and hybridized to the microarray
Hybridization protocol Hybridized probes were captured by streptavidin-phycoerythrin conjugates using Fluidics Station 450
Scan protocol GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA)
Description Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA).
Data processing QC, genotype calling and log2 ratios were produced in the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93% using the algorithm defaults. Genotype calls were made using the BRLMM algorithm. Parameter settings(CNAT 4.0.1): Transition decay 5 Mb, Median normalization and 0Mb smoothing factor. The reference set used consisted of 96 CEU samples from the HapMap project (
Submission date Oct 28, 2008
Last update date Dec 10, 2008
Contact name Richard Rosenquist Brandell
Organization name Uppsala University
Department Genetics and Pathology
Street address Rudbeck Laboratory
City Uppsala
ZIP/Postal code SE-751 85
Country Sweden
Platform ID GPL3718
Series (1)
GSE13557 Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms

Data table header descriptions
VALUE Genotype: AA,AB,BB,or No Call
B_Allele_Freq Estimate of B allele frequency
Log_R_Ratio GTYPE metric for relative signal intensity

Data table
ID_REF VALUE B_Allele_Freq Log_R_Ratio
SNP_A-1780520 BB NA -0.0617
SNP_A-1780618 AB 0.4646 -0.0722
SNP_A-1780632 AB 0.5339 -0.1599
SNP_A-1780654 AA NA -0.111
SNP_A-4192495 BB 0.8928 -0.2029
SNP_A-4192498 AB 0.5145 0.1687
SNP_A-1780732 BB 1.0157 -0.451
SNP_A-1780848 AB 0.4561 0.3234
SNP_A-1780985 BB 1.0552 0.0738
SNP_A-1781022 AA -0.0109 -0.1265
SNP_A-1781076 BB 1.0071 0.062
SNP_A-1781249 AB 0.569 0.0312
SNP_A-1781276 AA 0.1426 0.2991
SNP_A-1781302 BB 0.9517 -0.0283
SNP_A-1781510 AA 0.03 -0.1917
SNP_A-4192564 BB 0.9528 0.1333
SNP_A-1781614 AB 0.498 0.0075
SNP_A-1781633 BB 0.9487 0.4275
SNP_A-1781764 BB 1.0354 0.3325
SNP_A-1781829 AA NA 0.0682

Total number of rows: 262264

Table truncated, full table size 7915 Kbytes.

Supplementary file Size Download File type/resource
GSM337749.CEL.gz 26.8 Mb (ftp)(http) CEL
GSM337749.CHP.gz 4.1 Mb (ftp)(http) CHP
Processed data included within Sample table

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