|
| Status |
Public on Jun 28, 2013 |
| Title |
Case 372C |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Primary Bladder Cancer Sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell line: Primary Bladder Tumor Sample
tumor stage: T3 tumor stage
tumor grade: grade 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using a commercial kit, as described (DNeasy Blood & Tissue Kit; Qiagen, Hilden, Germany).
|
| Label |
Cy5
|
| Label protocol |
500ug of DNA extracted from the cell lines was labeled using the Enzymatic labeling protocol from Agilent, while in the case of primary tumors we use the non enzymatic Protocol for DNA extracted from Paraffin Embedded samples ULS Labeling Protocol (Agilent Inc., Palo Alto, CA)
|
| |
|
| Channel 2 |
| Source name |
Female DNA Pool
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
sample type: pooled control (reference) DNA
sample source: 20 healty donors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using a commercial kit, as described (DNeasy Blood & Tissue Kit; Qiagen, Hilden, Germany).
|
| Label |
Cy3
|
| Label protocol |
500ug of DNA extracted from the cell lines was labeled using the Enzymatic labeling protocol from Agilent, while in the case of primary tumors we use the non enzymatic Protocol for DNA extracted from Paraffin Embedded samples ULS Labeling Protocol (Agilent Inc., Palo Alto, CA)
|
| |
|
| |
| Hybridization protocol |
The Hybridization process was performed according to the manufacturer's protocol (Agilent Inc. , Palo Alto, Ca)
|
| Scan protocol |
Image scanning was performed using an Agilent Scanner (Agilent G2565AA) and microarray data were extracted using Agilent Feature Extraction v10.1 software.
|
| Data processing |
Data analysis and visualization were performed using Agilent DNA Analytics v4.0.76 Software. Copy number altered regions were detected using the Z-score (set as 4) and ADM-2 (set as 6) statistics provided by DNA Analytics.
|
| |
|
| Submission date |
Jul 18, 2011 |
| Last update date |
Jun 28, 2013 |
| Contact name |
Francesco Acquadro |
| E-mail(s) |
facquadro@cnio.es
|
| Phone |
+ (34) 917 328 000
|
| Fax |
+ (34) 912 246 980
|
| Organization name |
Centro Nacional de Investigaciones Oncologicas CNIO
|
| Department |
Molecular Cytogenetics
|
| Lab |
302A
|
| Street address |
calle de Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL5477 |
| Series (1) |
| GSE30754 |
Genomic Characterization of Bladder Cancer Cell Lines using CGH Arrays |
|
