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Sample GSM323875 Query DataSets for GSM323875
Status Public on Dec 10, 2008
Title 10_Agilent
Sample type genomic
 
Channel 1
Source name Blood
Organism Homo sapiens
Characteristics Gender: Female
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: Female
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 -0.081427202
A_14_P129311 0.360090606
A_14_P122429 -0.144403498
A_14_P102818 0.589084121
A_14_P134029 -0.144779885
A_14_P105506 0.09836143
A_14_P103853 -0.196382037
A_14_P116299 -0.087274849
A_14_P119386 0.056772994
A_14_P100003 0.03097993
A_14_P113759 0.308795361
A_14_P102175 -0.154670252
A_14_P124792 -0.174516982
A_14_P201436 -0.061509698
A_14_P131329 0.042258687
A_14_P122796 -0.033382676
A_14_P201183 -0.084198727
A_14_P132480 -0.470411249
A_14_P137941 0.077442465
A_14_P118943 0.046523798

Total number of rows: 181982

Table truncated, full table size 4788 Kbytes.




Supplementary file Size Download File type/resource
GSM323875.txt.gz 42.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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