|
| Status |
Public on Dec 10, 2008 |
| Title |
2_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 |
|
