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Sample GSM322218 Query DataSets for GSM322218
Status Public on Dec 10, 2008
Title 9_BAC
Sample type genomic
 
Channel 1
Source name Blood
Organism Homo sapiens
Characteristics Gender: Male, Tumor content: 90%
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 0.118551375
22668 -0.016541773
6764 -0.179721997
13919 -0.013392685
26310 0.023177393
8167 0.113603754
19040 -0.007256369
13568 -0.256760087
20144 -0.133336315
32004 0.044662012
33434 -0.027203519
17422 0.064051456
5024 0.267350736
13823 -0.087250846
266 0.231697553
996 0.094437736
12918 0.378390363
23855 0.713430325
3448 0.639627927
11285 0.03784762

Total number of rows: 31876

Table truncated, full table size 561 Kbytes.




Supplementary file Size Download File type/resource
GSM322218.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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