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Series GSE19539 Query DataSets for GSE19539
Status Public on Apr 19, 2010
Title Identification of Novel Oncogene Loci in Ovarian Cancer through Integrated Copy Number and Expression Analysis
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by SNP array
Summary Use of expression data to analyse ovarian cancer often yields long lists of genes that do not agree across various studies. Copy number however is more stable and can reliable predict important regions of change. Using matched copy number and expressiion data helps accurately identify novel drivers of ovarian cancer.
Overall design 72 tumours for copy number analysis with 57 matching blood normals. Out of these 72, 68 produced good quality RNA for expression arrays. These 68 array samples and have been run in 10 batches by the same user. Batch number is recorded under characteristics.

The SNP6_Normalised-Copy-number.csv file appended below contains the copy number ratios relative to matching normal samples or a pooled baseline. In this file, probes on Chromosome Y and the Mitochondrion (MT) have been removed and the probesets are organised first by Chromosome and then by start position. Annotations for this were mapped in Partek using the Affymetrix GenomewideSNP6, CN and SNP annotation files, release number 23.
Contributor(s) Ramakrishna M, Williams LH, Boyle SE, Bearfoot JL, Sridhar A, Gorringe KL, Campbell IG, Speed TP
Citation(s) 20386695
Submission date Dec 17, 2009
Last update date Nov 27, 2018
Contact name Manasa Ramakrishna
Organization name Peter MacCallum Cancer Centre
Street address St Andrew's Pl
City Melbourne
State/province Victoria
ZIP/Postal code 3002
Country Australia
Platforms (2)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (140)
GSM487253 Integrative genomics of ovarian cancer IC022 [HuGene-1_0-st]
GSM487254 Integrative genomics of ovarian cancer IC026 [HuGene-1_0-st]
GSM487255 Integrative genomics of ovarian cancer IC095 [HuGene-1_0-st]
BioProject PRJNA122315

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
GSE19539_RAW.tar 4.1 Gb (http)(custom) TAR (of CEL)
GSE19539_SNP6_Normalised-Copy-number.csv.gz 877.6 Mb (ftp)(http) CSV
Processed data included within Sample table
Processed data are available on Series record

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