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Sample GSM267503 Query DataSets for GSM267503
Status Public on May 31, 2008
Title Germ Cell Tumor, Histology 1, Biological replicate 5
Sample type RNA
 
Source name Seminoma (Dysgerminoma)
Organism Homo sapiens
Characteristics Pure, ovarian, female, age 13, stage 1
Treatment protocol N/A
Growth protocol Fresh frozen tumor material (pre-chemotherapy) was provided by the individual banking centers across the UK and from Düsseldorf, Germany
Extracted molecule total RNA
Extraction protocol TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Total RNA from each sample was used to prepare biotinylated target RNA in a one-cycle target labeling procedure, with minor modifications from the manufacturer’s recommendations available at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx. Briefly, 10 µg of cleaned total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 10-fold amplification of RNA.
 
Hybridization protocol Target cRNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) at Geneservice Ltd (Cambridge Science Park, Cambridge, UK), formerly MRC Geneservice. Briefly, spike controls were added to 15 µg fragmented cRNA before overnight hybridization with the Genechip Human Genome U133A arrays (Affymetrix).
Scan protocol Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner.
Description Gene expression data from malignant germ cell tumor
Data processing The array, once scanned, was used to generate an image file (with the extension .dat). GeneChip Operating Software (GCOS) was then used to compute cell intensity data from the image file and this data was saved in a file with the extension .cel. The .cel (CEL) files were provided by Geneservice Ltd and used for subsequent data analysis. Pre-processing of microarray data (including background correction and normalization) relied on the Robust Multi-Array Average (RMA) method within R.
 
Submission date Feb 22, 2008
Last update date Apr 24, 2008
Contact name Roger David Palmer
E-mail(s) rdp@hutchison-mrc.cam.ac.uk
Phone 0044 1223 763279
Fax 0044 1223 763284
Organization name Hutchison/MRC Research Centre
Department MRC Cancer Cell Unit
Lab 2.5
Street address Box 197 Hills Road
City Cambridge
ZIP/Postal code CB2 0XZ
Country United Kingdom
 
Platform ID GPL96
Series (1)
GSE10615 Pediatric malignant germ cell tumors show characteristic transcriptome profiles
Relations
Reanalyzed by GSM453861
Reanalyzed by GSE18155

Data table header descriptions
ID_REF
VALUE Post RMA normalization values

Data table
ID_REF VALUE
1007_s_at 8.408039409
1053_at 5.995115667
117_at 6.810388212
121_at 8.260558955
1255_g_at 4.535184379
1294_at 7.331567853
1316_at 5.7011608
1320_at 4.755587116
1405_i_at 7.087243206
1431_at 4.287563734
1438_at 6.684691506
1487_at 6.842158756
1494_f_at 6.343868463
1598_g_at 9.754661153
160020_at 8.461396374
1729_at 7.128448714
177_at 5.282454143
1773_at 5.597598551
179_at 8.119823964
1861_at 5.295909777

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM267503.cel.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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