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Sample GSM482090 Query DataSets for GSM482090
Status Public on May 01, 2013
Title MB 01
Sample type RNA
Source name Tumor material, snap frozen during surgery
Organism Homo sapiens
Characteristics tumour type: Medulloblastoma
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 7.191571
AFFX-BioB-M_at 7.77224
AFFX-BioB-3_at 6.975179
AFFX-BioC-5_at 8.709583
AFFX-BioC-3_at 9.180093
AFFX-BioDn-5_at 9.757151
AFFX-BioDn-3_at 10.98081
AFFX-CreX-5_at 12.05092
AFFX-CreX-3_at 12.5379
AFFX-DapX-5_at 6.124776
AFFX-DapX-M_at 8.035739
AFFX-DapX-3_at 9.210793
AFFX-LysX-5_at 3.753156
AFFX-LysX-M_at 4.648311
AFFX-LysX-3_at 5.846407
AFFX-PheX-5_at 3.952724
AFFX-PheX-M_at 4.773061
AFFX-PheX-3_at 6.379024
AFFX-ThrX-5_at 3.976163
AFFX-ThrX-M_at 4.78445

Total number of rows: 54675

Table truncated, full table size 1051 Kbytes.

Supplementary file Size Download File type/resource
GSM482090.CEL.gz 4.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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