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Sample GSM453855 Query DataSets for GSM453855
Status Public on Mar 15, 2010
Title Malignant germ cell tumor_YST-11 [mRNA]
Sample type RNA
Source name Yolk sac tumor replicate 10 of 10
Organism Homo sapiens
Characteristics tumor type: Yolk sac tumor
tumor composition: Pure
anatomical site: Ovary
gender: Female
age (yrs): 14
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: 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 GEO reference number: GSM267521
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
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
Reanalysis of GSM267521

Data table header descriptions
VALUE Post RMA normalization signal intensity

Data table
1007_s_at 8.728275881
1053_at 6.743090073
117_at 6.400637868
121_at 8.158516291
1255_g_at 4.241857232
1294_at 7.213778424
1316_at 5.518266111
1320_at 5.231209033
1405_i_at 4.246389488
1431_at 4.067946949
1438_at 7.344828473
1487_at 6.926783772
1494_f_at 6.163035977
1598_g_at 10.04750305
160020_at 8.852007526
1729_at 6.929565947
177_at 5.268040633
1773_at 5.935661255
179_at 8.785676228
1861_at 6.197196912

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM453855.cel.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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