NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM322216 Query DataSets for GSM322216
Status Public on Dec 10, 2008
Title 6_BAC
Sample type genomic
 
Channel 1
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. 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 0.113752587
22668 0.116907563
6764 -0.111925355
13919 0.133305079
26310 -0.119638472
8167 -0.031062233
19040 0.039722128
13568 0.005545318
20144 -0.046188868
32004 0.091338373
33434 -0.064462296
17422 0.150871506
5024 0.038237209
13823 0.1012834
266 -0.001717075
996 0.044212245
12918 null
23855 0.297685473
3448 0.331350937
11285 -0.157866411

Total number of rows: 31876

Table truncated, full table size 559 Kbytes.




Supplementary file Size Download File type/resource
GSM322216.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap