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Sample GSM1571006 Query DataSets for GSM1571006
Status Public on May 21, 2015
Title 4ep35
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): 29
gender: f
molecular subgroup: PF_EPN_B
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 2.5360529
1552829_at 2.722466024
1552867_at 3.572889668
1552961_at 1.378511623
1552974_at 0
1552975_x_at 2.321928095
1552976_at 5.274261661
1553083_at 2
1553208_s_at 1.201633861
1553275_s_at 2.350497247
1553355_at 0.137503524
1553356_at 0
1553372_at 2.350497247
1553398_at 0.485426827
1553439_at 2.584962501
1553456_at 3.432959407
1553462_at 1.263034406
1553498_at 3.232660757
1553547_at 3.62058641
1553882_at 2.169925001

Total number of rows: 54675

Table truncated, full table size 1177 Kbytes.




Supplementary file Size Download File type/resource
GSM1571006_dkfz1789.cel.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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