|
| Status |
Public on May 21, 2015 |
| Title |
Brain tumor 9533774101_R02C02 |
| Sample type |
genomic |
| |
|
| Source name |
brain tumor, infratentorial, PF-EPN-A, WHO grade 3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ependymal tumor
tumor type: primary
molecular subtype: PF-EPN-A
material: formalin-fixed, paraffin-embedded (FFPE)
location: 1
who grade: 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride. DNA was isolated from formalin-fixed and paraffin-embedded (FFPE) tissue using the blackPREP FFPE DNA Kit (Analytik Jena, Jena, Germany) according to the manufacturer's instructions.
|
| Label |
biotin/DNP
|
| Label protocol |
Illumina protocol.
|
| |
|
| Hybridization protocol |
Illumina protocol.
|
| Scan protocol |
Illumina iScan System according to the manufacturer's protocol.
|
| Description |
Methylation data from ependymal tumor sample.
Location: 1: infratentorial; 2: spinal; 3: supratentorial.
|
| Data processing |
Data analysis was performed using the open source statistical programming language R (R Core Team, 2014; http://www.R-project.org/). Raw data files generated by the iScan array scanner were read and preprocessed using the capabilities of the Bioconductor (Version 2.9) package minfi (Version 1.12; Aryee et al., 2014 (PMID 24478339)). With the minfi package using function 'preprocessIllumina', the same preprocessing steps, i.e., background subtraction and normalization using control probes, as in Illumina's GenomeStudio software were performed.
|
| |
|
| Submission date |
Jan 27, 2015 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Martin Sill |
| E-mail(s) |
m.sill@dkfz.de
|
| Organization name |
DKFZ
|
| Department |
Division of Pediatric Neurooncology
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE65362 |
Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. |
|
| Relations |
| Reanalyzed by |
GSE243240 |
