|
| Status |
Public on Jul 01, 2011 |
| Title |
CNS-PNET 05-0531 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human brain
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tumor type: Primitive Neuroectodermal Tumors of the Central Nervous System
|
| Growth protocol |
Fresh-frozen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)
|
| Label |
Cy3
|
| Label protocol |
The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
|
| |
|
| Channel 2 |
| Source name |
Control_DNA_Promega
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
gender: Female
|
| Growth protocol |
Fresh-frozen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)
|
| Label |
Cy5
|
| Label protocol |
The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
|
| |
|
| |
| Hybridization protocol |
The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
|
| Scan protocol |
All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.
|
| Data processing |
Agilent Feature Extraction Software (version 10.5.1.1) and Genomic Workbench software (Agilent Technologies Inc., Palo Alto, California, USA). Aberrant DNA copy number intervals identified using the Aberration Detection Method 2 (ADM-2), default threshold setting 6.0, and Fuzzy Zero correction algorithm applied. To ensure the exclusion of very low or very small aberrations, we added a custom-made aberration filter defining a region with a copy number aberration as a region with minimum five probes gained/lost and with minimum absolute average log2 ratio of 0.2 (gain) or -0.2 (loss). A loss defined as homozygous when the log2 ratio was lower than -1, and a gain was regarded as high level amplification when the log2 ratio was higher than 1.
|
| |
|
| Submission date |
Mar 03, 2011 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Hanne-Sofie S Dahlback |
| E-mail(s) |
h.s.s.dahlback@medisin.uio.no
|
| Organization name |
The Norwegian Radium Hospital
|
| Department |
Section for Cancer Cytogenetics
|
| Street address |
Montebello
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL10123 |
| Series (1) |
| GSE27671 |
Genomic Aberrations in Paediatric Gliomas and Embryonal Tumours |
|
