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Sample GSM482089 Query DataSets for GSM482089
Status Public on May 01, 2013
Title ATRT 01
Sample type RNA
Source name Tumor material, snap frozen during surgery
Organism Homo sapiens
Characteristics tumour type: atypical teratoid/rhabdoid tumour (ATRT)
Growth protocol Tumor material was removed during surgery then snap frozen
Extracted molecule total RNA
Extraction protocol RNA was extracted using the mirVana miRNA isolation kit (Ambion)
Label biotin
Label protocol Biotinylated cRNA was prepared from 5 mg RNA using the Affymetrix HT IVT labeling method (one cycle)
Hybridization protocol Labeled RNA was hybridized for 16 hours at 45 oC on the U133 plus 2 array. GeneChips were washed and stained in the fluidics station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip scanner 8000 with autoloader
Description no additional information
Data processing Raw data was analysed using Expression console. RMA was used to generate data for analysis. Processed data was analysed in Spotfire DecisionSite for Functional Genomics (TIBCO Software Inc.) for hierarchical clustering and priniciple component analysis. BRB Array Tools Software ver 3.7 ( was used for t-tests.
Submission date Dec 09, 2009
Last update date May 01, 2013
Contact name Hazel Anne Rogers
Organization name University of Nottingham
Department Clinical Sciences
Lab D30
Street address Medical School
City Nottingham
ZIP/Postal code NG7 2UH
Country United Kingdom
Platform ID GPL570
Series (1)
GSE19404 Gene expression analysis of primitive neuroectodermal tumors

Data table header descriptions
VALUE RMA signal intensity

Data table
AFFX-BioB-5_at 8.249229
AFFX-BioB-M_at 8.543803
AFFX-BioB-3_at 8.061331
AFFX-BioC-5_at 9.654644
AFFX-BioC-3_at 9.962499
AFFX-BioDn-5_at 10.59667
AFFX-BioDn-3_at 11.61579
AFFX-CreX-5_at 12.75532
AFFX-CreX-3_at 13.11669
AFFX-DapX-5_at 7.770232
AFFX-DapX-M_at 8.76966
AFFX-DapX-3_at 9.843154
AFFX-LysX-5_at 4.963673
AFFX-LysX-M_at 5.555282
AFFX-LysX-3_at 7.000835
AFFX-PheX-5_at 5.3852
AFFX-PheX-M_at 5.680848
AFFX-PheX-3_at 6.695126
AFFX-ThrX-5_at 5.766809
AFFX-ThrX-M_at 6.327786

Total number of rows: 54675

Table truncated, full table size 1052 Kbytes.

Supplementary file Size Download File type/resource
GSM482089.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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