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Series GSE24601 Query DataSets for GSE24601
Status Public on Feb 01, 2011
Title Metastatic and Nonmetastatic canine soft tissue sarcoma comparison
Organism Canis lupus familiaris
Experiment type Expression profiling by array
Summary We hypothesize that there is a gene signature which will improve our ability to predict development of metastatic disease in STS patients. The objective of this study was to determine the feasibility of using cDNA microarray and quantitative real-time PCR (qRT-PCR) analysis to determine gene expression patterns in metastatic versus non-metastatic canine STSs, given the inherent heterogeneity of this group of tumors. Five STSs from dogs with metastatic disease were evaluated in comparison to eight STSs from dogs without metastasis. Tumor RNA was extracted, processed and labeled for application to the Affymetrix Canine Genechip 2.0 Array. Array fluorescence was normalized using D-Chip software and data analysis was performed with JMP/Genomics. Differential gene expression was validated using qRT-PCR. Over 200 genes were differentially expressed at a false discovery rate of 5%. Differential gene expression was validated for five genes upregulated in metastatic tumors. Quantitative RT-PCR confirmed increased relative expression of all five genes of interest in the metastatic STSs. Our results demonstrate that microarray and qRT-PCR are feasible methods for comparing gene signatures in canine STSs. Further evaluation of differences in gene expression between metastatic and non-metastatic STSs is likely to identify genes important in the development of metastatic disease and improve our ability to prognosticate for individual patients.
 
Overall design Comparison of metastatic and non-metastatic (defined as no metastasis for at least one year) untreated tumor biopsies.
 
Contributor(s) Hauck M, Snyder S, Mahoney J, Fisher J
Citation(s) 21076837
Submission date Oct 08, 2010
Last update date Mar 22, 2012
Contact name Marlene Hauck
E-mail(s) marlene_hauck@ncsu.edu
Organization name North Carolina State University
Department Clinical Sciences
Street address 4700 Hillsborough Street
City Raleigh
State/province NC
ZIP/Postal code 27606
Country USA
 
Platforms (1)
GPL3738 [Canine_2] Affymetrix Canine Genome 2.0 Array
Samples (13)
GSM606558 MET1
GSM606560 MET2
GSM606561 MET3
Relations
BioProject PRJNA132393

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
GSE24601_RAW.tar 52.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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