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Sample GSM1570972 Query DataSets for GSM1570972
Status Public on May 21, 2015
Title 8ep6
Sample type RNA
 
Source name Frozen ependymal tumor tissue
Organism Homo sapiens
Characteristics tissue: Ependymal tumor
primary/relapse: primary
brain location: posterior fossa
age at diagnosis (years): 12
gender: f
molecular subgroup: PF_EPN_A
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 1.137503524
1552829_at 4.968090752
1552867_at 5.311067102
1552961_at 3.560714954
1552974_at 0
1552975_x_at 2
1552976_at 5.232660757
1553083_at 0.584962501
1553208_s_at 0.485426827
1553275_s_at 4.161887682
1553355_at 1.678071905
1553356_at 0.847996907
1553372_at 3.03562391
1553398_at 2.786596362
1553439_at 2.459431619
1553456_at 4.137503524
1553462_at 2.5360529
1553498_at 4.554588852
1553547_at 4.209453366
1553882_at 3.053111336

Total number of rows: 54675

Table truncated, full table size 1194 Kbytes.




Supplementary file Size Download File type/resource
GSM1570972_dkfz1587.cel.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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