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Sample GSM322209 Query DataSets for GSM322209
Status Public on Dec 10, 2008
Title 4_BAC
Sample type genomic
 
Channel 1
Source name Blood
Organism Homo sapiens
Characteristics Gender: Male, Tumor Content: 93%
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 -0.004729052
22668 0.07357756
6764 0.073801279
13919 0.019538842
26310 0.125783478
8167 0.144105794
19040 -0.098652519
13568 0.004700032
20144 -0.024611323
32004 0.281928731
33434 null
17422 0.079979436
5024 -0.122852053
13823 -0.243074834
266 -0.064431083
996 0.065369931
12918 -0.047645703
23855 0.112212425
3448 0.154569754
11285 -0.065176938

Total number of rows: 31876

Table truncated, full table size 558 Kbytes.




Supplementary file Size Download File type/resource
GSM322209.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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