|
| Status |
Public on May 09, 2012 |
| Title |
Early-stage breast cancer 188 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Early-stage breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Breast
tumor stage: 2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
1 µg of genomic DNA were labeled with fluorescent dye at 37°C for 2 hours. BioPrime aCGH labeling system (Invitrogen) was used for labeling step.
|
| |
|
| Channel 2 |
| Source name |
genomic DNA from frozen normal breast tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Breast
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
1 µg of genomic DNA were labeled with fluorescent dye at 37°C for 2 hours. BioPrime aCGH labeling system (Invitrogen) was used for labeling step.
|
| |
|
| |
| Hybridization protocol |
Human Cot-1 DNA (Connectagen) and DIG hybridization buffer (Roche) were added. The labeled DNA solution applied on the array and incubated for 48 hours at 37ºC in MAUI hybridization machine (BioMicro). After hybridization, slides were washed sequentially.
|
| Scan protocol |
The arrays were scanned using GenePix 4000B scanner (Axon Instruments)
Feature extraction was processed using Axon GenePix Pro version 6.0.
|
| Description |
BRC188.gpr
|
| Data processing |
Normalization and re-alignment of raw array CGH data were performed using the web-based array CGH analysis interface, ArrayCyGHt. We used a print-tip Loess normalization method.
|
| |
|
| Submission date |
May 08, 2012 |
| Last update date |
May 09, 2012 |
| Contact name |
SeungHyun Jung |
| E-mail(s) |
hyun@catholic.ac.kr
|
| Phone |
82-2-2258-7509
|
| Organization name |
Catholic University of Korea
|
| Department |
Department of Biochemistry
|
| Street address |
catholic university, medical college, banpo-dong
|
| City |
seoul |
| State/province |
seoul |
| ZIP/Postal code |
06591 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6254 |
| Series (1) |
|
