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Sample GSM322211 Query DataSets for GSM322211
Status Public on Dec 10, 2008
Title 8_BAC
Sample type genomic
 
Channel 1
Source name Blood
Organism Homo sapiens
Characteristics Gender: Female, Tumor content: 87%
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions. An additional purification step was performed using Phase Lock Gel Heavy (Eppendorf).
Label Cy3 (sample)
Label protocol Copy number profiling was performed using tiling 32K BAC as previously described (PMID:17334996). Samples were labelled with Cy3, and male reference DNA (Promega) with Cy5.
 
Channel 2
Source name male reference DNA (Promega)
Organism Homo sapiens
Characteristics male reference DNA (Promega)
Extracted molecule genomic DNA
Extraction protocol see Promega's website
Label Cy5 (reference)
Label protocol Copy number profiling was performed using tiling 32K BAC as previously described (PMID:17334996). Samples were labelled with Cy3, and male reference DNA (Promega) with Cy5.
 
 
Hybridization protocol Samples were hybridized and washed as previously described (PMID:17334996).
Scan protocol Arrays were scanned on a Agilent microarray scanner (Agilent Technologies).
Description Genomic DNA extracted from CLL patients was analyzed using tiling 32K BAC microarrays.
Data processing Image data was analyzed using Genepix Pro 4.0 (Axon Instruments). Result files were loaded into BASE (http://base.thep.lu.se) where they were filtered, lowess normalized and segmented using Circular Binary Segmentation (CBS, DNAcopy package).
 
Submission date Sep 18, 2008
Last update date Dec 10, 2008
Contact name Richard Rosenquist Brandell
E-mail(s) richard.rosenquist@genpat.uu.se
Organization name Uppsala University
Department Genetics and Pathology
Street address Rudbeck Laboratory
City Uppsala
ZIP/Postal code SE-751 85
Country Sweden
 
Platform ID GPL4723
Series (1)
GSE13557 Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms

Data table header descriptions
ID_REF
VALUE Normalized log2 ratios (sample / reference)

Data table
ID_REF VALUE
27039 0.016063219
22668 -0.056933457
6764 -0.133587184
13919 -0.052366572
26310 0.051633404
8167 0.022410362
19040 -0.071278281
13568 0.033716964
20144 -0.080353779
32004 0.070320377
33434 0.065716843
17422 -0.048141845
5024 -0.027323176
13823 -0.015210801
266 -0.076116301
996 -0.177762334
12918 0.185981882
23855 0.721074328
3448 0.60452942
11285 -0.410842922

Total number of rows: 31876

Table truncated, full table size 553 Kbytes.




Supplementary file Size Download File type/resource
GSM322211.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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