|
| Status |
Public on Jan 10, 2014 |
| Title |
Sample 5_Agilent 108K |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
TUMOR, MYC-NEG LYMPHOMA CASE 8
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: MYC-negative B-cell lymphoma
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 8 B-cell lymphoma samples using the phenol-chloroform extraction method according to previously published protocols with minor modification. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis. All extracted DNAs had at least a PCR control gene band of 200 bp.
|
| Label |
Cy5
|
| Label protocol |
As per manufacturer (Agilent)
|
| |
|
| Channel 2 |
| Source name |
Normal genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sex-matched control DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 8 B-cell lymphoma samples using the phenol-chloroform extraction method according to previously published protocols with minor modification. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis. All extracted DNAs had at least a PCR control gene band of 200 bp.
|
| Label |
Cy3
|
| Label protocol |
As per manufacturer (Agilent)
|
| |
|
| |
| Hybridization protocol |
The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.
|
| Scan protocol |
Scanned on an Agilent G2565B scanner.
|
| Description |
Case 9_S01_CGH_107_Sep09_1_4
|
| Data processing |
Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and default settings of Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA). All alterations were analyzed by visual inspection of two different observers.
|
| |
|
| Submission date |
May 30, 2013 |
| Last update date |
Jan 10, 2014 |
| Contact name |
Itziar Salaverria |
| E-mail(s) |
isalaver@clinic.cat
|
| Organization name |
Hospital Clínic
|
| Street address |
Rossello 153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE47506 |
Recurrent 11q aberrations in MYC-neg mature aggressive B-cell lymphomas resembling BL |
| GSE47508 |
A recurrent 11q aberration pattern characterizes a subset of MYC-negative mature aggressive B-cell lymphomas resembling Burkitt lymphoma |
|
