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Sample GSM323879 Query DataSets for GSM323879
Status Public on Dec 10, 2008
Title 1_Agilent
Sample type genomic
 
Channel 1
Source name Blood
Organism Homo sapiens
Characteristics Gender: Male
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-dUTP (sample)
Label protocol Copy number profiling was performed using Agilent 185K 60-mer oligonucleotide CGH microarrays. Samples were labelled with Cy3-dUTP, and male reference DNA (Promega) with Cy5-dUTP.
 
Channel 2
Source name Promega male reference DNA
Organism Homo sapiens
Characteristics Gender: Male
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 Cy5-dUTP (reference)
Label protocol Copy number profiling was performed using Agilent 185K 60-mer oligonucleotide CGH microarrays. Samples were labelled with Cy3-dUTP, and male reference DNA (Promega) with Cy5-dUTP.
 
 
Hybridization protocol Samples were hybridized and washed according to manufacturer's protocol (Ver 4.0, June 2006).
Scan protocol Arrays were scanned on a Agilent microarray scanner (Agilent Technologies).
Description Genomic DNA extracted from CLL patients was analyzed using Agilent 185K 60-mer oligonucleotide CGH microarrays.
Data processing Image data was analyzed using Feature Extraction ver 9.1 (Agilent Technologies). 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 23, 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 GPL5149
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
A_14_P106403 -0.215845275
A_14_P129311 0.048914098
A_14_P122429 -0.194449187
A_14_P102818 0.013193918
A_14_P134029 -0.026068123
A_14_P105506 0.073185352
A_14_P103853 0.271496454
A_14_P116299 -0.127633045
A_14_P119386 0.061636247
A_14_P100003 0.15112775
A_14_P113759 -0.014737358
A_14_P102175 -0.253730913
A_14_P124792 -0.092953837
A_14_P201436 0.313071334
A_14_P131329 0.202522112
A_14_P122796 -0.288371113
A_14_P201183 -0.023411476
A_14_P132480 -0.19209371
A_14_P137941 0.140898754
A_14_P118943 -0.024562437

Total number of rows: 181982

Table truncated, full table size 4785 Kbytes.




Supplementary file Size Download File type/resource
GSM323879.txt.gz 42.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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