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Sample GSM1570988 Query DataSets for GSM1570988
Status Public on May 21, 2015
Title 13ep3
Sample type RNA
Source name Frozen ependymal tumor tissue
Organism Homo sapiens
Characteristics tissue: Ependymal tumor
primary/relapse: relapse
brain location: spinal
age at diagnosis (years): 34
gender: f
molecular subgroup: SP_MPE
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
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
VALUE MAS5.0 signal intensity, log2 transformed

Data table
1552563_a_at 1.070389328
1552829_at 5.303780748
1552867_at 3.689299161
1552961_at 3.754887502
1552974_at 2.981852653
1552975_x_at 3.378511623
1552976_at 5.678071905
1553083_at 4.03562391
1553208_s_at 3.523561956
1553275_s_at 4.263034406
1553355_at 1
1553356_at 0.925999419
1553372_at 3.807354922
1553398_at 3.62058641
1553439_at 4.548436625
1553456_at 4.350497247
1553462_at 2.510961919
1553498_at 4.336283388
1553547_at 4.371558863
1553882_at 2.906890596

Total number of rows: 54675

Table truncated, full table size 1196 Kbytes.

Supplementary file Size Download File type/resource
GSM1570988_dkfz1676.cel.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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