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Sample GSM412300 Query DataSets for GSM412300
Status Public on Nov 23, 2009
Title SCAN303
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics tissue: Blood
phenotype: CLL sample
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 Affymetric Genotyping Console 3.0.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93
 
Submission date Jun 03, 2009
Last update date Nov 23, 2009
Contact name Anders Isaksson
E-mail(s) anders.isaksson@medsci.uu.se
Organization name Uppsala University
Street address Akademiska sjukhuset ing61 3tr
City Uppsala
ZIP/Postal code 75185
Country Sweden
 
Platform ID GPL3718
Series (1)
GSE16406 Copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia

Data table header descriptions
ID_REF
VALUE Genotyping Console metric for relative signal intensity
BAF B allele frequency

Data table
ID_REF VALUE BAF
SNP_A-1780270 -0.016433 0.49383
SNP_A-1780272 -0.078232 1.1137
SNP_A-1780285 0.086952 NaN
SNP_A-1780286 0.05545 0.64373
SNP_A-1780287 0.10419 -0.070618
SNP_A-1780289 -0.014603 0.97008
SNP_A-1780292 -0.1026 1.0959
SNP_A-1780294 0.027226 1.0005
SNP_A-1780295 0.20799 1.1627
SNP_A-1780300 0.25866 NaN
SNP_A-1780302 -0.67435 0.99893
SNP_A-1780303 -0.11473 NaN
SNP_A-1780304 -0.036592 -0.008553
SNP_A-1780305 -0.15652 0.50008
SNP_A-1780311 -0.10132 -0.12534
SNP_A-1780312 -0.14864 0.4885
SNP_A-1780313 -0.066166 -0.077332
SNP_A-1780316 -0.0059006 1.0455
SNP_A-1780318 0.080717 NaN
SNP_A-1780320 0.38251 0.93227

Total number of rows: 262217

Table truncated, full table size 7836 Kbytes.




Supplementary file Size Download File type/resource
GSM412300.CEL.gz 24.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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