|
| Status |
Public on Jul 01, 2016 |
| Title |
breast cancer 9 |
| Sample type |
genomic |
| |
|
| Source name |
primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
|
| Treatment protocol |
none
|
| Growth protocol |
primary formalin fixed parafffin embedded tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DANN was extracted from macrodissected with DNAeasy blood and tissue kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
as given by the 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 7G.
|
| Description |
hybridized to [OncoScan] Affymetrix OncoScan array
|
| Data processing |
CEL files were generated after scanning by the Affymetrix GeneChip Command Console (AGCC). These CEL files were further processed using OncoScan Console software version 1.3.0.39 to produce OSCHP files.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal. Data was analyzed using Chromosome Analysis Suite (ChAS) version 3.1.0.15.
|
| |
|
| Submission date |
Jun 30, 2016 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Doris Johanna Steinemann |
| E-mail(s) |
steinemann.doris@mh-hannover.de
|
| Phone |
+495115324669
|
| Organization name |
Hannover Medical School
|
| Department |
Institute of Human Genetics
|
| Lab |
Array-Lab
|
| Street address |
Carl-Neuberg-Str.1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE83916 |
Oncoscan for HER2 copy number assessment |
|
