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Sample GSM453853 Query DataSets for GSM453853
Status Public on Mar 15, 2010
Title Malignant germ cell tumor_YST-8 [mRNA]
Sample type RNA
Source name Yolk sac tumor replicate 8 of 10
Organism Homo sapiens
Characteristics tumor type: Yolk sac tumor
tumor composition: Mixed, within mature teratoma
anatomical site: Sacrococcygeal
gender: Female
age (yrs): 2
tumor stage: 4
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: GSM267523
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 GSM267523

Data table header descriptions
VALUE Post RMA normalization signal intensity

Data table
1007_s_at 8.758355583
1053_at 6.926725034
117_at 6.389803883
121_at 8.162578121
1255_g_at 4.222476294
1294_at 6.652838365
1316_at 5.524944783
1320_at 4.987149593
1405_i_at 4.538576801
1431_at 3.92570034
1438_at 6.68729464
1487_at 7.062460431
1494_f_at 6.342972022
1598_g_at 9.21672137
160020_at 8.078095628
1729_at 6.987999099
177_at 5.600379267
1773_at 5.982779391
179_at 8.543214793
1861_at 5.811519099

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM453853.cel.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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