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Sample GSM453858 Query DataSets for GSM453858
Status Public on Mar 15, 2010
Title Malignant germ cell tumor_Sem-15 [mRNA]
Sample type RNA
 
Source name Seminoma replicate 3 of 6
Organism Homo sapiens
Characteristics tumor type: Seminoma
tumor composition: Pure
anatomical site: Central nervous system
gender: Male
age (yrs): 16
tumor stage: 1
Growth protocol Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.
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 GEO reference number: GSM267506
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) was performed using the Bioconductor package Robust Multi-Array Average (RMA) in the statistical software environment R.
 
Submission date Sep 17, 2009
Last update date Mar 11, 2010
Contact name Matthew Jonathan Murray
E-mail(s) mjm16@cam.ac.uk
Phone 07976413769
Organization name MRC Cancer Cell Unit
Department MRC/Hutchison Research Centre
Lab 2.5
Street address Box 197, Hills Road
City Cambridge
ZIP/Postal code CB2 0XZ
Country United Kingdom
 
Platform ID GPL96
Series (1)
GSE18155 Malignant Germ Cell Tumors Display Common microRNA Profiles Resulting in Global Changes in Expression of mRNA Targets
Relations
Reanalysis of GSM267506

Data table header descriptions
ID_REF
VALUE Post RMA normalization signal intensity

Data table
ID_REF VALUE
1007_s_at 9.521929175
1053_at 6.370635038
117_at 6.535655636
121_at 8.153540659
1255_g_at 4.393935283
1294_at 7.689197747
1316_at 5.226898851
1320_at 4.692680091
1405_i_at 6.886157713
1431_at 4.365243969
1438_at 6.535519928
1487_at 6.906995329
1494_f_at 6.02481271
1598_g_at 9.737956328
160020_at 7.914645506
1729_at 6.887296652
177_at 5.160174531
1773_at 6.27148754
179_at 8.250582601
1861_at 5.331321498

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM453858.cel.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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