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Sample GSM267505 Query DataSets for GSM267505
Status Public on May 31, 2008
Title Germ Cell Tumor, Histology 1, Biological replicate 7
Sample type RNA
Source name Seminoma (Germinoma)
Organism Homo sapiens
Characteristics Pure, CNS, female, age 10, 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: 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 ( 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
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
Reanalyzed by GSM453857
Reanalyzed by GSE18155

Data table header descriptions
VALUE Post RMA normalization values

Data table
1007_s_at 9.445790055
1053_at 6.720365367
117_at 6.435011059
121_at 8.222880934
1255_g_at 4.287104638
1294_at 7.384951148
1316_at 5.524890942
1320_at 4.857691046
1405_i_at 7.028241036
1431_at 4.302030855
1438_at 6.409355421
1487_at 7.238640556
1494_f_at 6.090884189
1598_g_at 9.346024232
160020_at 8.024430448
1729_at 7.168038749
177_at 5.138419495
1773_at 6.227267074
179_at 8.501322577
1861_at 5.289971264

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM267505.cel.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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