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Sample GSM1593318 Query DataSets for GSM1593318
Status Public on May 21, 2015
Title Brain tumor 9968646163_R04C01
Sample type genomic
 
Source name brain tumor, infratentorial, PF-EPN-A, WHO grade 2
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: 2
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

Supplementary data files not provided
Processed data are available on Series record

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