|
| Status |
Public on Nov 26, 2011 |
| Title |
05-53384a12 (M) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Commercial DNAs
|
| Organism |
Homo sapiens |
| Characteristics |
source: Clontech Laboratories Inc
gender: male
|
| Treatment protocol |
Fresh-frozen (Tianjin cohort) or formalin-fixed and paraffin-embedded (MD Anderson cohort)
|
| Growth protocol |
Human primary tumor samples obtained by surgical resection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy kit from Qiagen cat# 69506 with minor modifications as mentioned in the Agilent aCGH protocol ULS Labeling Version 3.0.
|
| Label |
Cy3
|
| Label protocol |
Standard protocol for labeling genomic DNA
|
| |
|
| Channel 2 |
| Source name |
MPNST
|
| Organism |
Homo sapiens |
| Characteristics |
source: MDACC
gender: male
|
| Treatment protocol |
Fresh-frozen (Tianjin cohort) or formalin-fixed and paraffin-embedded (MD Anderson cohort)
|
| Growth protocol |
Human primary tumor samples obtained by surgical resection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy kit from Qiagen cat# 69506 with minor modifications as mentioned in the Agilent aCGH protocol ULS Labeling Version 3.0.
|
| Label |
Cy5
|
| Label protocol |
Standard protocol for labeling genomic DNA
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized according to Agilent's protocol
|
| Scan protocol |
Arrays were scanned with Agilent's scanner using manufacturer's instructions.
|
| Data processing |
Data were extracted using Agilent Feature Extraction software (CGH-v4_91). Logratios were lowess-normalized. Ratio is always tumor/ref; dye-swaps were performed as necessary.
|
| |
|
| Submission date |
Nov 22, 2011 |
| Last update date |
Nov 29, 2011 |
| Contact name |
Antti Ylipää |
| E-mail(s) |
antti.ylipaa@tut.fi
|
| Organization name |
Tampere University of Technology
|
| Street address |
Korkeakoulunkatu 1
|
| City |
Tampere |
| ZIP/Postal code |
33101 |
| Country |
Finland |
| |
|
| Platform ID |
GPL5477 |
| Series (1) |
| GSE33881 |
Genomic characterization of the MPNST |
|
