|
| Status |
Public on Jan 01, 2013 |
| Title |
M13 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Medulloblastoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue using the QIAamp Blood Mini Kit using a modified protocol incorporating deparaffinization and protease digestion (QIAGEN, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
Control and tumor DNA were labeled by random priming with CY3- and CY5-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue using the QIAamp Blood Mini Kit using a modified protocol incorporating deparaffinization and protease digestion (QIAGEN, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
Control and tumor DNA were labeled by random priming with CY3- and CY5-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
The labeled DNA were purified with the Millipore Amicon 30 kDa centrifugal filter device (Billerica, MA) and mixed in equal proportion for hybridization to the array in the presence of Cot-1 DNA (Invitrogen, Carlsbad, CA) using the Agilent Oligo aCGH Hybridization Kit.
|
| Scan protocol |
Washed slides were scanned using the Agilent G2565CA Microarray Scanner. Microarray TIFF (.tif)
|
| Description |
comparison between MBL and normal genomic DNA
|
| Data processing |
Images were processed and analyzed with Agilent CytoGenomics v1.5 software.
|
| |
|
| Submission date |
Nov 01, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Matija Snuderl |
| E-mail(s) |
MSnuderl@partners.org
|
| Organization name |
MAssachusetts General Hospital
|
| Department |
Pathology
|
| Street address |
55 Fruit St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL16237 |
| Series (1) |
| GSE41990 |
Deep Sequencing Identifies IDH1 R132S Mutation in Adult Medulloblastoma (CGH) |
|
