|
| Status |
Public on Jul 01, 2014 |
| Title |
Urothelial bladder tumor B1829s1 |
| Sample type |
genomic |
| |
|
| Source name |
Bladder Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bladder Carcinoma
cell type: Carcinoma cells
gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from the paired-WGS set was extracted from frozen tumor tissue and blood using the Puregene DNA purification kit (Gentra Systems, Minneapolis, MN, USA). Amplification Kit, GE Healthcare)
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Data processing |
Call and signal intensities were done using the birdseedv2 algorithm. For copy number, CEL files were analysed using the arome.affymetrix R package. All probes from each allele were combined in one value per probeset (SNP or CN). Segmentation was done using the Rseg R package.
The log2 ratio was calculated as the log2 ratio between the theta estimates from the tumor sample and the theta estimates from the blood sample from the same patient for chromosomes 1 to 22 and chromosome X.
|
| |
|
| Submission date |
Sep 06, 2013 |
| Last update date |
Jul 01, 2014 |
| Contact name |
Philippe Lamy |
| E-mail(s) |
PHILIPPE.LAMY@SVF.AU.DK
|
| Organization name |
MOMA
|
| Department |
Department of molecular medecine
|
| Street address |
Brendstrupgårdsvej 100
|
| City |
Aarhus N |
| ZIP/Postal code |
8200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE50667 |
The pattern of genomic instability during bladder cancer progression (part 2) |
| GSE50668 |
The pattern of genomic instability during bladder cancer progression |
|
