|
| Status |
Public on Jul 07, 2013 |
| Title |
Metastatic Bladder Cancer 1351 |
| Sample type |
genomic |
| |
|
| Source name |
Metastatic Bladder Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
unique_patient_id: 1351
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 251
vital_status: deceased
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from tumors using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA)
|
| Label |
ULS-Cy5
|
| Label protocol |
The Genomic DNA ULS labeling kit for FFPE Samples (Agilent Technologies, Inc., Palo Alto, CA) was used to chemically label 500ng of DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) following the manufacturer's protocol
|
| |
|
| Hybridization protocol |
Genomic DNA samples were hybridized to the array using an Agilent microarray hybridization chamber for 40 hours in a Robbins Scientific oven with rotation at 20 rpm at 65°C
|
| Scan protocol |
Post-hybridization, the slides were washed and scanned using an Agilent DNA microarray scanner
|
| Description |
Genomic DNA isolated from metastatic bladder cancer
|
| Data processing |
CGH Analytics software (version 3.4, Agilent Technologies, CA) was used to analyze the aCGH data
Copy numbers were segmented using the GLAD algorithm. The 'spanishaCGH.glad.txt' are the segmented data (like the Level 3 data in TCGA), calculated with the GLAD algorithm: Sample ID, Chromosome, Start, End, Number of Probes in the segment, log2 copy number ratio of the segment (available on a Series records).
|
| |
|
| Submission date |
Jul 11, 2012 |
| Last update date |
Jul 07, 2013 |
| Contact name |
Markus Riester |
| E-mail(s) |
markus@jimmy.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Biostatistics & Computational Biology
|
| Lab |
Michor
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL10150 |
| Series (2) |
| GSE39281 |
DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Agilent] |
| GSE39282 |
DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer |
|
