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Sample GSM1570895 Query DataSets for GSM1570895
Status Public on May 21, 2015
Title 3ep54
Sample type RNA
 
Source name Frozen ependymal tumor tissue
Organism Homo sapiens
Characteristics tissue: Ependymal tumor
primary/relapse: primary
brain location: supratentorial
age at diagnosis (years): 8
gender: f
molecular subgroup: ST_EPN_RELA
Treatment protocol Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
Extracted molecule total RNA
Extraction protocol Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
Label Biotin
Label protocol Affymetrix protocol
 
Hybridization protocol Affymetrix protocol
Scan protocol Affymetrix protocol
Description MAS5.0 normalized data
Data processing For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
 
Submission date Dec 22, 2014
Last update date May 21, 2015
Contact name Marcel Kool
E-mail(s) m.kool@dkfz.de
Organization name German Cancer Research Center DKFZ
Department Pediatric Neurooncology
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL570
Series (1)
GSE64415 Gene expression data from ependymal tumor samples

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity, log2 transformed

Data table
ID_REF VALUE
1552563_a_at 0.378511623
1552829_at 4.121015401
1552867_at 4.169925001
1552961_at 1.887525271
1552974_at 2.655351829
1552975_x_at 0
1552976_at 4.232660757
1553083_at 0.485426827
1553208_s_at 3.217230716
1553275_s_at 4.03562391
1553355_at 0
1553356_at 0
1553372_at 0
1553398_at 3
1553439_at 3.64385619
1553456_at 3.185866545
1553462_at 1.485426827
1553498_at 3.292781749
1553547_at 2.655351829
1553882_at 1.485426827

Total number of rows: 54675

Table truncated, full table size 1175 Kbytes.




Supplementary file Size Download File type/resource
GSM1570895_dkfz0136.cel.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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