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Series GSE41120 Query DataSets for GSE41120
Status Public on Sep 28, 2012
Title Molecular Characterization of 126 Intermediate Risk Prostate Cancer Patient Samples
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary The primary objective of this study was to correlate genetic alterations from Hh pathway genes with biochemical free relapse rate.
 
Overall design aCGH data of 126 intermediate risk men with histologically confirmed adenocarcinoma of the prostate who had chosen radical radiotherapy as their primary treatment between 1996-2006.

Please note that the '2014-11-11_IGRT_aCGH_gene_matrix_GEO.csv' was generated as following;
The gene matrix is a gene by sample matrix, where -1 corresponds to deletion, 0 to copy neutral, and 1 to gain. The normalized data on GEO was converted from hg18 to hg19 using the liftOver tool from UCSC (version dated 2011-11-27). Fragments overlapping centromeres, telomeres, or other gaps in the hg18 build were trimmed conservatively (regions were shortened rather than elongated). To generate contiguous CNA regions, probe-based CNA calls were collapsed with neighbouring probes within the same chromosome with the same copy number. CNA regions with only one supporting probe were removed. In addition, any CNAs found entirely within centromeres or telomeres, as defined by the UCSC ~Qgap~R table, were removed. CNA regions were intersected with a merged and collapsed version of the RefSeq gene annotation (GRCh37/hg19) to generate gene-based CNA calls. This gene list was further filtered to match the published gene list from the MSKCC radical prostatectomy cohort

The 'IGRT_full_clinical_info.txt' file contanis additional/updated clinical data (including survival).
 
Contributor(s) McKee CM, Muschel RJ
Citation(s) 23041623, 25415046
Submission date Sep 24, 2012
Last update date Jul 31, 2019
Contact name Igor Jurisica
Organization name Princess Margaret Cancer Center
Department TMDT 11-413
Street address 101 College St.
City Toronto
State/province ON
ZIP/Postal code M5G1L7
Country Canada
 
Platforms (1)
GPL2616 BCCRC Lam SMRTr array
Samples (126)
GSM1009939 Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 1
GSM1009940 Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 2
GSM1009941 Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 3
Relations
BioProject PRJNA176223

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
GSE41120_2014-11-11_IGRT_aCGH_gene_matrix_GEO.csv.gz 385.6 Kb (ftp)(http) CSV
GSE41120_IGRT_full_clinical_info.txt.gz 3.7 Kb (ftp)(http) TXT
GSE41120_non-normalized_data.txt.gz 28.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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