|
| Status |
Public on Mar 31, 2017 |
| Title |
Tumor_8828 (aCGH) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
8p11-p12 amplification: Amplified
age: 78
pt status: pT3
lymph node status: pN1
er status: neg
pgr status: neg
her2 status: pos
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification
|
| Label |
Cy3
|
| Label protocol |
Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively
|
| |
|
| Channel 2 |
| Source name |
Normal female genomic DNA reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Normal female genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification
|
| Label |
Cy5
|
| Label protocol |
Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively
|
| |
|
| |
| Hybridization protocol |
Hybridization probes were denatured, preannealed, and cohybridized to arrays pretreated with the Universal Microarray Hybridization Kit. Following hybridization, slides were washed at room temperature and dried by centrifugation.
|
| Scan protocol |
Images and raw signal intensities were acquired using an Agilent G2505B DNA microarray scanner and GenePix Pro 6.0.1.22 image analysis software
|
| Data processing |
Pin-based LOWESS normalized, spot intensities representing the tumor (cy3) and reference (cy5) channels were background-corrected by subtracting the median background from the median foreground signal intensities. BASE database used.
|
| |
|
| Submission date |
Mar 31, 2017 |
| Last update date |
Mar 31, 2017 |
| Contact name |
Toshima Z. Parris |
| E-mail(s) |
toshima.parris@oncology.gu.se
|
| Organization name |
University of Gothenburg
|
| Department |
Department of Oncology
|
| Lab |
Sahlgrenska Cancer Center
|
| Street address |
Medicinaregatan 1G, 6th floor
|
| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9077 |
| Series (2) |
| GSE97292 |
Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [aCGH] |
| GSE97293 |
Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas |
|
