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Series GSE25720 Query DataSets for GSE25720
Status Public on Jul 12, 2012
Title Affymetrix SNP 6.0 array data for chordoma samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Chordomas are rare, low to intermediate grade malignant bone tumors of the axial skeleton, believed to originate from the notochord. Treatment options are limited and mainly restricted to surgical excision, as chordomas have been proven to be largely resistant to conventional ionizing radiation and chemotherapy. Therefore a new cell line was established. The cell line has been characterized by immunohistochemistry,western blot and karyotyping using cobra fish technology. Copy number variations (CNV) and loss-of heterozygosity (LOH) from fibroblasts, tumor tissue, low and high cell line passage was evaluted by using Affymetrix 6.0SNP Arrays. DNA isolated from the patients MNCs was used as control. The cell line MUG-Chor1 is highly similar to genetic profiles of chordomas and provides therefore a powerful tool for further investigations.
Overall design Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines.
Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.
Contributor(s) Rinner B, Gülly C
Citation(s) 22002331
Submission date Nov 30, 2010
Last update date Nov 27, 2018
Contact name Carina Fischer
Organization name ZMF
Street address Stiftingtalstr. 24
City Graz
ZIP/Postal code 8010
Country Austria
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (4)
GSM631720 tumor
GSM631721 blood cells
GSM631722 chordoma cell line p5
BioProject PRJNA133847

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25720_RAW.tar 318.6 Mb (http)(custom) TAR (of CEL, CHP, CNCHP)
Processed data included within Sample table
Processed data provided as supplementary file

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