|
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: 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 |
GSM453857 |
Reanalyzed by |
GSE18155 |