|
| Status |
Public on Dec 02, 2011 |
| Title |
TAX577691 (HumanOmni2.5) |
| Sample type |
genomic |
| |
|
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Breast cancer (HER2+)
er: er_pos
osbin: 1
os: 2.912328767
age: 30.6037
ln: 0
size_mm: 30
primary: 1
grade: 2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip
|
| |
|
| Hybridization protocol |
Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip
|
| Scan protocol |
Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip
|
| Data processing |
Copy number (Log R) and B allele frequency estimates were obtained from GenomeStudio (Illumina). Genomic profiles from 2.5M data were partitioned using the R implementation (DNAcopy) of Circular Binary Segmentation (CBS) with an alpha value of 0.001. Change points were analyzed using the SDundo option in CBS with a standard deviation threshold of 1.
|
| |
|
| Submission date |
Aug 24, 2011 |
| Last update date |
Dec 02, 2011 |
| Contact name |
Johan Staaf |
| Organization name |
SCIBLU - Swegene Centre for Integrative Biology at Lund University
|
| Street address |
Medicon Village
|
| City |
Lund |
| ZIP/Postal code |
SE-223 81 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13314 |
| Series (1) |
| GSE31645 |
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer |
|
